Anaerobic Bacteria Research Articles

Enhanced steel corrosion inhibition through microbially induced carbonate precipitation with facultative anaerobic denitrifying bacterium

Denitrification processes are increasingly studied as a promising alternative to ureolytic microbially induced carbonate precipitation (MICP). This study investigates the capabilities of the newly isolated denitrifying bacterium, Stutzerimonas stutzeri CF3, in promoting calcium carbonate precipitation and enhancing steel corrosion resistance under both aerobic and anaerobic conditions. The facultative anaerobe was tested across a range of environmental parameters including pH levels (7.5–11.5), C/N ratios (5−15), NaCl salinity (0–5 %), and Ca²⁺ concentrations (0–30 mmol), to determine its adaptability and effectiveness in precipitating calcium carbonate. Our findings reveal that S. stutzeri CF3 not only survives but thrives under extreme conditions, demonstrating significant nitrate removal and robust calcium carbonate precipitation, particularly in high salinity and variable pH environments. Furthermore, the study examines the implications of S. stutzeri CF3 on steel corrosion, particularly Q235 steel, using Tafel polarization techniques, demonstrating enhanced corrosion resistance. These results underscore the dual utility of S. stutzeri CF3 in microbial self-healing concrete applications, pointing to its potential to improve the durability and integrity of construction materials by leveraging its versatile metabolic pathways.

A Pyroptosis-Inducing Arsenic(III) Nanomicelle Platform for Synergistic Cancer Immunotherapy.

Immunogenic cell death (ICD) could activate anti-tumor immune responses, which is highly attractive for improving cancer treatment effectiveness. Here, this work reports a multifunctional arsenic(III) allosteric inhibitor Mech02, which induces excessive accumulation of 1O2 through sensitized biocatalytic reactions, leading to cell pyroptosis and amplified ICD effect. After Mech02 is converted to Mech03, it could actualize stronger binding effects on the allosteric pocket of pyruvate kinase M2, further interfering with the anaerobic glycolysis pathway of tumors. The enhanced DNA damage triggered by Mech02 and the pyroptosis of cancer stem cells provide assurance for complete tumor clearance. In vivo experiments prove nanomicelle Mech02-HA NPs is able to activate immune memory effects and raise the persistence of anti-tumor immunity. In summary, this study for the first time to introduce the arsenic(III) pharmacophore as an enhanced ICD effect initiator into nitrogen mustard, providing insights for the development of efficient multimodal tumor therapy agents.

Integrated metabolomics analysis of chill-stored rose shrimp (Parapenaeus longirostris) treated with different pressure levels of high hydrostatic pressure by 1H-NMR spectroscopy.

The antimicrobial effects of high hydrostatic pressure (HHP) treatments on chill-stored seafood are well-documented, while their impact on the metabolic profile of seafood, especially the metabolome of fish flesh, and remains underexplored. Addressing this gap, this study investigates the effects of HHP on the metabolome of chill-stored rose shrimp by conducting multivariate data analysis based on untargeted proton nuclear magnetic resonance observations. Vacuum-packed rose shrimp samples were subjected to HHP at 0, 400, 500, and 600MPa for 10 min and then stored at 2-4°C. The microorganism analysis and metabolic analysis were carried out on days 1 and 14. HHP treatment effectively deactivated Lactobacillus spp., Escherichia coli, Pseudomonas spp., total Coliforms, and sulfite-reducing anaerobic bacteria. Consequently, HHP treatment significantly reduced the formation rate of decay-related metabolites, such as hypoxanthine, trimethylamine, and biogenic amines, which exhibited significant accumulation in untreated samples. Multivariate unsupervised analyses provided insights into the overall changes in the metabolite profile induced by HHP. Metabolic pathway analysis revealed several pathways underlying spoilage, including pyruvate metabolism, valine, leucine, and isoleucine biosynthesis, purine metabolism, methane metabolism, glycine, serine, and threonine metabolism, citrate cycle (TCA cycle), glycolysis/gluconeogenesis, alanine, aspartate, and glutamate metabolism, sulfur metabolism, pantothenate and CoA biosynthesis, glutathione metabolism, and glyoxylate and dicarboxylate metabolism. Importantly, these pathways underwent alterations due to the application of HHP, particularly at high-pressure levels. In summary, the results unveil the potential mechanisms of HHP effects on chill-stored rose shrimps.

Screening of As-Resistant Bacterial Strains from the Bulk Soil and the Rhizosphere of Mycorrhizal Pteris vittata Cultivated in an Industrial Multi-Polluted Site

Arsenic (As) contamination poses significant environmental and health concerns globally, particularly in regions with high exposure levels due to anthropogenic activities. As phytoremediation, particularly through the hyperaccumulator fern Pteris vittata, offers a promising approach to mitigate arsenic pollution. Bacteria and mycorrhizal fungi colonizing P. vittata roots are involved in As metabolism and resistance and plant growth promotion under stressful conditions. A total of 45 bacterial strains were isolated from bulk soil and the rhizosphere of mycorrhizal P. vittata growing in an industrial As-polluted site. Bacteria were characterized by their plant-beneficial traits, tolerance to sodium arsenate and arsenite, and the occurrence of As-resistant genes. This study highlights differences between the culturable fraction of the microbiota associated with the rhizosphere of mycorrhizal P. vittata plants and the bulk soil. Moreover, several strains showing arsenate tolerance up to 600 mM were isolated. All the bacterial strains possessed arsC genes, and about 70% of them showed arrA genes involved in the anaerobic arsenate respiration pathway. The possible exploitation of such bacterial strains in strategies devoted to the assisted phytoremediation of arsenic highlights the importance of such a study in order to develop effective in situ phytoremediation strategies.

Electroactive biofilters outperform inert biofilters for treating surfactant-polluted wastewater by means of selecting a low-growth yield microbial community

Electrobioremediation is one of the most innovative disciplines for treating organic pollutants and it is based on the ability of electroactive bacteria to exchange electrons with electroconductive materials. Electroactive biofilters have been demonstrated to be efficient for treating urban wastewater with a low footprint; however, their application can be expanded for treating industrial wastewater containing significant concentrations (2.4 %vol) of commercial surfactants (containing lauryl sulfate, lauryl ether sulfate, cocamydopropyl betaine, and dodecylbenzene sulfonate, among others). Our electroactive biofilter outperformed a conventional inert biofilter made of gravel for all tested conditions, reaching removal rates as high as 4.5 kg COD/m3bed·day and withstood Organic Loading Rates as high as 9 Kg COD/m3·d without significantly affecting removal efficiency. The biomass accumulation reduced available bed volume in the electroactive biofilter just by 39 %, while the gravel biofilter decreased by 80 %. Regarding microbial communities, anaerobic and electroactive bacteria represented a substantial proportion of the total population in the electroactive biofilter. Pseudomonas was the dominant genus, while Cupriavidus, Shewanella, Citrobacter, Desulfovibrio, and Arcobacter were potential electroactive strains found in relevant proportions. The microbial community’s composition might be the key to understanding how high removal rates can coexist with limited biomass production, making electroactive biofilters a promising strategy to overcome classical biofilter limitations.

A geographical paradox: microbiological profile and antibiotic resistance of diabetic foot infection in North West England

AbstractBackground: The microbiological composition of diabetic foot infection (DFI) and its antimicrobial resistance exhibit variations in different parts of the world.Aims: This study aimed to shed light on the microbial load associated with DFI and the patterns of antibiotic resistance in Northwest England.Methods: This was a retrospective descriptive study that included 67 patients (55 male [78.6%]). The mean age at diagnosis was 45.6 years (standard deviation, 15.8). The culture of deep tissue samples was analysed together with antibiotic resistance.Results: A total of 114 causative pathogens were identified. Of note, 40 patients (60.00%) had polymicrobial infections. Moreover, 58.77% of the microbial cohort was composed of gram‐positive bacteria. Staphylococcus spp. were found in 32 patients (47.76%) and were the most prevalent pathogen in our cohort. Anaerobic bacteria were found in 17 patients (25.37%) and were the second most common pathogen in our cohort. Corynebacterium spp., Streptococcus spp. and Enterococcus spp. were identified in 11 (16.42%), 10 (14.93%) and 9 (13.43%) patients, respectively. Among the gram‐negative bacteria, Escherichia spp. were found in 7 patients (10.45%), Enterobacter spp. were found in 6 patients (8.96%), Klebsiella spp. were found in 4 patients (5.97%), Proteus spp. were found in 4 patients (5.97%) and Alcaligenes spp. were found in 2 patients (2.99%). The remaining less common organisms collectively accounted for 1.49% prevalence. Regarding antibiotic therapy, the highest resistance was observed for ciprofloxacin (12 [17.91%]), followed by amoxicillin (11 [16.42%]), penicillin (10 [14.93%]), clarithromycin (7 [10.45%]), trimethoprim (7 [10.45%]), doxycycline (6 [8.96%]) and piperacillin/tazobactam (5 [7.46%]).Conclusions: In contrast to the predominant aerobic gram‐negative bacteria in Asia, the Middle East and Africa, our study found a paradoxically higher prevalence of gram‐positive and anaerobic bacteria in North West England. Moreover, our study found a high incidence of resistance to ciprofloxacin and amoxicillin.

Clinical and microbiological characteristics of anaerobic bacteremia during 1994–2019: A Danish population-based cohort study

ObjectivesBacteremia with anaerobic bacteria is generally a marker of severe prognosis. However, population-based data is lacking. Our aim was to describe the epidemiology and the 30-day mortality rate of anaerobic bacteremia in a Danish population-based setting. MethodsIn this population-based cohort study, all first-time episodes of anaerobic bacteremia from the North Denmark Bacteremia Research Database during 1994–2019 were identified. Information on comorbidities, discharge diagnoses, and mortality was retrieved. 30-day mortality rates were calculated and a multivariate logistic regression analysis to identify risk factors for death was performed. Results1750 episodes with anaerobic bacteremia were identified, corresponding to an incidence rate of 12.5 per 100,000 inhabitants (increasing from 11.2 in 1994–2014 to 17.7 in 2015–2019). Of these episodes, a third were polymicrobial, and the majority (70 %) of patients had one or more comorbid conditions. Abdominal infection was the source of bacteremia in 61 % of patients, while it was unknown for 15 %. The most frequently isolated genera were Bacteroides (45 %), Clostridium (20 %) and Fusobacterium (6 %). The overall crude 30-day mortality rate was 27 %, but rates were even higher for patients of high age, with liver disease, and solid tumors. The odds ratio (OR) for 30-day mortality was 1.32 for Clostridium species, and 1.27 for polymicrobial bacteremia with aerobic bacteria. ConclusionsThe incidence rate of anaerobic bacteremia increased, and the 30-day mortality rate remained high during the study period. Multiple factors influence 30-day mortality rates, including high age, liver disease, solid tumor, polymicrobial bacteremia, and bacteremia with Clostridium species.

SkinCom, a synthetic skin microbial community, enables reproducible investigations of the human skin microbiome

Existing models of the human skin have aided our understanding of skin health and disease. However, they currently lack a microbial component, despite microbes' demonstrated connections to various skin diseases. Here, we present a robust, standardized model of the skin microbial community (SkinCom) to support invitro and invivo investigations. Our methods lead to the formation of an accurate, reproducible, and diverse community of aerobic and anaerobic bacteria. Subsequent testing of SkinCom on the dorsal skin of mice allowed for DNA and RNA recovery from both the applied SkinCom and the dorsal skin, highlighting its practicality for invivo studies and -omics analyses. Furthermore, 66% of the responses to common cosmetic chemicals invitro were in agreement with a human trial. Therefore, SkinCom represents a valuable, standardized tool for investigating microbe-metabolite interactions and facilitates the experimental design of invivo studies targeting host-microbe relationships.

Structural, Biochemical, and Phylogenetic Analysis of Bacterial and Fungal Carbohydrate Esterase Family 15 Glucuronoyl Esterases in the Rumen

Glucuronoyl esterases (GEs) are carbohydrate active enzymes in carbohydrate esterase family 15 which are involved in the hydrolysis of lignin-carbohydrate complexes. They are encoded by a wide range of aerobic and anaerobic fungi and bacteria inhabiting diverse environments. The rumen microbiome is a complex microbial community with a wide array of enzymes that specialize in deconstructing plant cell wall carbohydrates. Enzymes from the rumen tend to show low similarity to homologues found in other environments, making the rumen microbiome a promising source for the discovery of novel enzymes. Using a combination of phylogenetic and structural analysis, we investigated the structure-function relationship of GEs from the rumen bacteria Fibrobacter succinogenes and Ruminococcus flavefaciens, and from the rumen fungus, Piromyces rhizinflata. All adopt a canonical α/β hydrolase fold and possess a structurally conserved Ser-His-Glu/Asp catalytic triad. Structural variations in the enzymes are localized to loops surrounding the active site. Analysis of the active site structures in these enzymes emphasized the importance of structural plasticity in GEs with non-canonical active site conformations. We hypothesize that interkingdom HGT events may have contributed to the diversity of GEs in the rumen, and this is demonstrated by the phylogenetic and structural similarity observed between rumen bacterial and fungal GEs. This study advances our understanding of the structure-function relationship in glucuronoyl esterases and illuminates the evolutionary dynamics that contribute to enzyme diversity in the rumen microbiome.

Effect of Ozone on Enterobacteriaceae Counts in Wheat Grain, Alfalfa, Radish, Broccoli Seeds and Sprouts

Abstract The sprouts of various seeds have garnered considerable regard amid consumers due to its verdure, crispiness, and germination potential, offering a cost-effective and straightforward process. The moist and warm conditions are very conducive to germination, fostering the growth of microorganisms and thereby raising food safety concerns. The aim of the study was to investigate the impact of ozone on Enterobacteriaceae counts by subjecting wheat (Triticum aestivum) grains, alfalfa (Medicago sativa), radish (Raphanus sativus) and broccoli (Brassica oleracea) seeds to ozone gas treatment. Additionally, the grain and seeds were rinsed with ozonated water during germination. Three different treatment methods were employed for seeds and grains. In the first method, samples were exposed to ozone gas at 20 ppm for 10 minutes, with subsequent rinsing every 12 hours during germination until the rinse water appeared visually clean, at a concentration of 2.0 mg L−1 of ozone. The second method involved rinsing with ozonated water at a concentration of 2.0 mg L−1 for durations of 20, 40, and 60 minutes. The third method - treated with ozone gas at 50 ppm and the exposure time of 1, 2, 3, 4 and 5 h. Untreated samples were used as controls. Evaluation of the samples revealed that Enterobacteriaceae was virtually undetectable in dry seeds. However, after 72 hours of germination in both the control and ozone-treated sprouts and following 7 days of storage at 4±2 °C, Enterobacteriaceae were found at an average of 7 to 8.1 log CFU g−1 in all samples, irrespective of the treatment method. Additionally, mould was observed only in wheat and radish sprouts during the assessment period. The study showed that there was no significant reduction in the number of mesophilic aerobic and facultative anaerobic microorganisms, moulds and Enterobacteriaceae then treated with ozone gas.

Competitive Binding Kinetics of Methylmercury-Cysteine with Dissolved Organic Matter: Critical Impacts of Thiols on Adsorption and Uptake of Methylmercury by Algae.

Complexes with low-molecular-weight thiols are crucial species of methylmercury (MeHg) excreted by anaerobic Hg-methylating microbes, notably, MeHg-cysteine (MeHg-Cys). As MeHg-Cys diffuses into surface water, it would undergo a ligand exchange process with dissolved organic matter (DOM) under nonsulfidic conditions, inevitably altering MeHg speciation and bioavailability to phytoplankton. In this study, we investigated the competitive binding kinetics between MeHg-Cys and Suwannee River natural organic matter, and their influence on the adsorption and uptake of MeHg by the cyanobacterium, Synechocystis sp. PCC6803. Liquid chromatography-inductively coupled plasma mass spectrometry was employed to monitor the kinetics processes involving competition of DOM with Cys for MeHg binding, which revealed that competitive binding kinetics were dictated by the abundance of thiol moieties in DOM. Thiol concentrations of 0.97 and 49.34 μmol of thiol (g C)-1 resulted in competitive binding rate constant (k values) of 0.30 and 3.47 h-1, respectively. Furthermore, the time-dependent competitive binding of DOM toward MeHg-Cys significantly inhibited MeHg adsorption and uptake by cyanobacteria, an effect that was amplified by an increased thiol abundance in DOM. These findings offer valuable insights into the kinetic characteristics of MeHg's fate and transport, as well as their impact on bioconcentration in aquatic organisms within natural aquatic ecosystems.

Prosthetic joint infection caused by Mediterraneibacter gnavus following total knee arthroplasty, challenges in anaerobic bacteria identification

BackgroundMediterraneibacter gnavus is a Gram positive, non-sporulated, obligate anaerobe diplococci. It was first described in 1974 by Moore et al. (under the name Ruminococcus gnavus) from faeces and contents of the gastrointestinal tract of humans. It is a relatively common member of the human gut microbiota, nevertheless its role as a pathogenic bacterium has not been completely elucidated yet and it seems to depend on numerous factors, including those of the host. Here we present a case of prosthetic joint infection following total knee arthroplasty by M. gnavus.Case presentationA 74 years old patient was admitted to the emergency department presenting with acute onset of left knee pain and swelling 20 days after total left knee arthroplasty. Follow-up revealed erythema and oedema without signs of fluctuation or purulent discharge from the surgical wound and elevated inflammatory reactants. Synovial fluid was taken for bacterial culture and antibiotic treatment with ceftazidime and daptomycin was established. Examination of the synovial fluid revealed abundant polymorphonuclear leucocytes, without visualizing bacteria. After four days of incubation, anaerobic culture exhibit growth of small, grey, umbilicated colonies in pure culture on Schaedler agar. The microorganism was identified as R. gnavus by MALDI-TOF (Bruker Daltonics) and M. gnavus by 16S ribosomal bacterial sequencing. The isolated showed susceptibility to the most commonly used anaerobicidal antibiotics except for clindamycin. Surgical treatment and infection source control included DAIR (debridement, antibiotics, and implant retention) and vacuum assisted therapy. The patient was discharged after six weeks with a 3-month course of oral amoxicillin as consolidation therapy. Subsequent follow-up revealed adequate wound healing with no signs of infection.ConclusionsMediterraneibacter gnavus have been reported as the causal microorganism in a range of human infections, nevertheless its identification remains challenging. Infection of prosthetic joints by anaerobic microorganisms is uncommon and is not considered in its empirical antibiotic treatment, thus, correct and swift identification of anaerobic bacteria in these cases is paramount.

Phase variable colony variants are conserved across Gardnerella spp. and exhibit different virulence-associated phenotypes.

The Gardnerella genus, comprising at least 13 species, is associated with the polymicrobial disorder bacterial vaginosis (BV). However, the details of BV pathogenesis are poorly defined, and the contributions made by individual species, including Gardnerella spp., are largely unknown. We report here that colony phenotypes characterized by size (large and small) and opacity (opaque and translucent) are phase variable and are conserved among all tested Gardnerella strains, representing at least 10 different species. With the hypothesis that these different variants could be an important missing piece to the enigma of how BV develops in vivo, we characterized their phenotypic, proteomic, and genomic differences. Beyond increased colony size, large colony variants showed reduced vaginolysin secretion and faster growth rate relative to small colony variants. The ability to inhibit the growth of Neisseria gonorrhoeae and commensal Lactobacillus species varied by strain and, in some instances, differed between variants. Proteomics analyses indicated that 127-173 proteins were differentially expressed between variants. Proteins with increased expression in large variants of both strains were associated with amino acid and protein synthesis and protein folding, whereas those increased in small variants were related to nucleotide synthesis, phosphate transport, ABC transport, and glycogen breakdown. Furthermore, whole genome sequencing analyses revealed an abundance of genes associated with variable homopolymer tracts, implicating slipped strand mispairing in Gardnerella phase variation and illuminating the potential for previously unrecognized heterogeneity within clonal populations. Collectively, these results suggest that phase variants may be primed to serve different roles in BV pathogenesis.IMPORTANCEBacterial vaginosis is the most common gynecological disorder in women of childbearing age. Gardnerella species are crucial to the development of this dysbiosis, but the mechanisms involved in the infection are not understood. We discovered that Gardnerella species vary between two different forms, reflected in bacterial colony size. A slow-growing form makes large amounts of the toxin vaginolysin and is better able to survive in human cervix tissue. A fast-growing form is likely the one that proliferates to high numbers just prior to symptom onset and forms the biofilm that serves as a scaffold for multiple BV-associated anaerobic bacteria. Identification of the proteins that vary between different forms of the bacteria as well as those that vary randomly provides insight into the factors important for Gardnerella infection and immune avoidance.

Enhanced methane production from anaerobic digestion of waste activated sludge with weak magnetic field: Insights into performances and mechanisms

The impact of weak magnetic field (WMF) on anaerobic digestion (AD) performance of waste activated sludge (WAS) and underlying mechanism were investigated. Results showed that WMF significantly stimulated the methane yield by 12.9∼25.1% with 15 and 30 mT WMF addition, but high WMF (60 mT) attenuated the positive effect. The WMF enriched the anaerobic microbes, especially the acetoclastic and hydrogenotrophic methanogen. Additionally, the WMF dramatically facilitated the metabolic pathways of key enzymes for methanogenesis, which was validated by the significant increase of absolute abundance of anaerobic functional genes (mcrA). The enzyme activities of ATP and F420 were also significantly promoted by 30 mT WMF, but high WMF (60 mT) resulted in increased activity of lactate dehydrogenase. This study reveals that low WMF can promote AD performance of WAS through enhancing microbial activities especially methanogen, but high WMF leads to the loss of cell membrane integrity and attenuates its positive effect.

The effect of the probiotic bacteria <i>Akkermansia Muciniphila</i> in intestinal homeostasis and dss-induced inflammation in mice

Akkermansia muciniphila is a Gram-negative anaerobic bacterium, a component of the normal human intestinal microbiota. A decrease in the presence of this bacterium is associated with pathologies, including metabolic disorders, intestinal inflammation and colorectal cancer. A. muciniphila is a probiotic approved for patients with diabetes and obesity. In recent years, A. muciniphila was studied in the control of intestinal inflammation and colorectal cancer. The exact mechanisms of A. muciniphila action remain unclear, while the use of different administration protocols shows different effects in mouse models of colitis and colorectal cancer. We reported that A. muciniphila has distinct effects on intestinal mucin production depending on viable or pasteurized form of bacteria. Another factor affecting the outcome of the A. muciniphila administration is the number of bacteria. To address how the dose of bacteria may affect the severity of acute intestinal inflammation wild-type mice were subjected to daily oral injections with 10⁸ CFU or 109 CFU of viable A. muciniphila for two weeks; the control group was injected with PBS. After that, groups were subjected to the induction of acute colitis by adding 7% DSS to drinking water for five days. 8 days after the onset of colitis induction, a morphometric assessment of the colitis severity was performed. Mice given a high dose of A. muciniphila (109 CFU) were found to be protected from developing severe colitis. RT-PCR analysis of colon samples from mice receiving a high dose of bacteria showed an increase in the gene expression of antimicrobial peptides, IL-17A, IL-17F. Interestingly, the protective effect of A. muciniphila was observed only in a high dose group, but not in a low dose group. Our data suggest that A. muciniphila provides the protective effect in colitis and highlight the importance of selecting the dose of the bacterium for proper interpretation.

Feasibility and mechanism exploration of enhancing short chain fatty acid production assisted by nitrate photolysis during sludge fermentation

Seeking for the eco-friendly and low-cost pretreatment technology has become the prerequisite for the efficient release of the embedded organics in waste activated sludge (WAS), further for the higher production of short chain fatty acids (SCFAs) via anaerobic fermentation. Nitrate, which can produce reactive oxygen species (ROS) and reactive nitrogen species (RNS) during photolysis, may have the positive effect on WAS disintegration and organics degradation, while its performance and mechanism for WAS treatment is still unknown. This study investigated the feasibility of the nitrate photolysis on WAS disintegration and SCFAs production, and elucidated the underlying mechanism. Results showed that the highest acidification rate (26.6 h−1) and short-chain fatty acid (SCFAs) production (5370.6 mg COD/L) were achieved at 8 d in the nitrate photolysis group (Nitrate-UV) during the anaerobic fermentation, significantly promoted by 2.3 and 12.7 folds than that of Control (raw WAS). Acetic acid (HAc) and propionic acid (HPr) accounted for 89.1 % and 90.1 % in Nitrate-UV and Nitrate group (sole nitrate addition), which were much higher than that obtained in UV and Control. HO• and O2•− were the main contributors compared with NO2•, ONOO– and NO• on the release and bioconversion of the soluble organics. Microbial community and metagenomics revealed the promotion of nitrate photolysis on anaerobic fermentation bacteria (AFB) and nitrate reducing bacteria (NRB), as well as the gene abundance related to the metabolic pathways of glycolysis, amino acid, acetate and nitrogen metabolism, which jointly devoted to the SCFAs enhancement during the anaerobic fermentation.

Comparative Genomic Analysis of Campylobacter rectus and Closely Related Species.

Campylobacter rectus is a gram-negative, anaerobic bacterium strongly associated with periodontitis. It also causes various extraoral infections and is linked to adverse pregnancy outcomes in humans and murine models. C. rectus and related oral Campylobacters have been termed "emerging Campylobacter species" because infections by these organisms are likely underreported. Previously, no comparative methods have been used to analyze more than single C. rectus strains and until recently, very few C. rectus genomes have been publicly available. More sequenced genomes and comparative analyses are needed to study the genomic features and pathogenicity of this species. We sequenced eight new C. rectus strains and used comparative methods to identify regions of interest. An emphasis was put on the type III flagellar secretion system (T3SS), type IV secretion system (T4SS), and type VI secretion system (T6SS) because these protein complexes are important for pathogenesis in other Campylobacter species. RAST, BV-BRC, and other bioinformatics tools were used to assemble, annotate, and compare these regions in the genomes. The pan-genome of C. rectus consists of 2670 genes with core and accessory genomes of 1429 and 1241 genes, respectively. All isolates analyzed in this study have T3SS and T6SS hallmark proteins, while five of the isolates are missing a T4SS system. Twenty-one prophage clusters were identified across the panel of isolates, including four that appear intact. Overall, significant genomic islands were found, suggesting regions in the genomes that underwent horizontal gene transfer. Additionally, the high frequency of CRISPR arrays and other repetitive elements has led to genome rearrangements across the strains, including in areas adjacent to secretion system gene clusters. This study describes the substantial diversity present among C. rectus isolates and highlights tools/assays that have been developed to permit functional genomic studies. Additionally, we have expanded the studies on C. showae T4SS since we have two new C. showae genomes to report. We also demonstrate that unlike C. rectus , C showae does not demonstrate evidence of intact T6SS except for the strain CAM. The only strain of sequenced C. massilensis has neither T4SS or T6SS.

Comparison of the Direct Identification and Short-Term Incubation Methods for Positive Blood Cultures via MALDI-TOF Mass Spectrometry.

Timely pathogen identification in bloodstream infections is crucial for patient care. A comparison is made between positive blood culture (BC) pellets from serum separator tubes using a direct identification (DI) method and colonies on agar plates from a short-term incubation (STI) method with a matrix-assisted laser desorption/ionization Biotyper for the evaluation of 354 monomicrobial BCs. Both the DI and STI methods exhibited similar identification rates for different types of bacteria, except for Gram-positive and anaerobic bacteria. The DI method's results aligned closely with the STI method's results for Enterobacterales, glucose-non-fermenting Gram-negative bacilli (GNB), and carbapenem-resistant Enterobacterales. The DI method exhibited high concordance with the conventional method for GNB identification, achieving 88.2 and 87.5% accuracy at the genus and species levels, respectively. Compared with the STI method, the DI method showed a less successful performance for Gram-positive bacterial identification (50.5 vs. 71.3%; p < 0.01). The DI method was useful for anaerobic bacterial identification of slow-growing microorganisms without any need for colony growth, unlike in the STI method (46.7 vs. 13.3%; p = 0.04). However, both methods could not identify yeast in positive BCs. Overall, the DI method provided reliable results for GNB identification, offering many advantages over the STI method by significantly reducing the turnaround time and enabling quicker pathogen identification in positive BCs.

Lactate-mediated mixotrophic co-cultivation of Clostridium drakei and recombinant Acetobacterium woodii for autotrophic production of volatile fatty acids

BackgroundAcetogens, a diverse group of anaerobic autotrophic bacteria, are promising whole-cell biocatalysts that fix CO2 during their growth. However, because of energetic constraints, acetogens exhibit slow growth and the product spectrum is often limited to acetate. Enabling acetogens to form more valuable products such as volatile fatty acids during autotrophic growth is imperative for cementing their place in the future carbon neutral industry. Co-cultivation of strains with different capabilities has the potential to ease the limiting energetic constraints. The lactate-mediated co-culture of an Acetobacterium woodii mutant strain, capable of lactate production, with the Clostridium drakei SL1 type strain can produce butyrate and hexanoate. In this study, the preceding co-culture is characterized by comparison of monocultures and different co-culture approaches.ResultsC. drakei grew with H2 + CO2 as main carbon and energy source and thrived when further supplemented with D-lactate. Gas phase components and lactate were consumed in a mixotrophic manner with acetate and butyrate as main products and slight accumulation of hexanoate. Formate was periodically produced and eventually consumed by C. drakei. A lactate-mediated co-culture of the A. woodii [PbgaL_ldhD_NFP] strain, engineered for autotrophic lactate production, and C. drakei produced up to 4 ± 1.7 mM hexanoate and 18.5 ± 5.8 mM butyrate, quadrupling and doubling the respective titers compared to a non-lactate-mediated co-culture. Further co-cultivation experiments revealed the possible advantage of sequential co-culture over concurrent approaches, where both strains are inoculated simultaneously. Scanning electron microscopy of the strains revealed cell-to-cell contact between the co-culture partners. Finally, a combined pathway of A. woodii [PbgaL_ldhD_NFP] and C. drakei for chain-elongation with positive ATP yield is proposed.ConclusionLactate was proven to be a well-suited intermediate to combine the high gas uptake capabilities of A. woodii with the chain-elongation potential of C. drakei. The cell-to-cell contact observed here remains to be further characterized in its nature but hints towards diffusive processes being involved in the co-culture. Furthermore, the metabolic pathways involved are still speculatory for C. drakei and do not fully explain the consumption of formate while H2 + CO2 is available. This study exemplifies the potential of combining metabolically engineered and native bacterial strains in a synthetic co-culture.

Petrocella pelovolcani sp. nov., an Alkaliphilic Anaerobic Bacterium Isolated from Terrestrial Mud Volcano

Diversity of extremophilic microorganisms in mud volcanoes is largely unexplored. Here we report the isolation of a novel alkaliphilic, mesophilic, fermentative bacterium (strain FN5sucT) from a terrestrial mud volcano located at the Taman Peninsula, Russia. Cells of strain FN5sucT are gram-stain-positive, non-sporeforming, motile rods. The temperature range for growth is 10–37°C, with an optimum at 30°C. The pH range for growth is 7.5–10.0, with an optimum at pH 9.0. The isolate utilizes various organic polymeric substances, organic acids, carbohydrates, and proteinaceous compounds. The end products of carbohydrates fermentation are acetate, CO2 and trace amounts of H2 and formate. The major cellular fatty acid compounds are C16:0, C16:1 ω7c, and monounsaturated dimethyl acetal C14:1. Phylogenetic analysis reveals that strain FN5sucT is most closely related to Petrocella atlantisensis = DSM 105309T (98.4% 16S rRNA gene identity). The total size of the genome of strain FN5sucT is 3.35 Mb, and a genomic DNA G+C content is 37.0 mol %. The genome contains complete glycolisis/glyconeogenesis pathway. We propose to assign strain FN5sucT to the genus Petrocella, as a new species, Petrocella pelovolcani sp. nov. The type strain is FN5sucT (=DSM 113898T = UQM 41591T).