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BMC Microbiology Oct 2023Anaerobes are normal flora of the human body. However, they can cause serious infections in humans. Anaerobic bacteria are known to cause respiratory infections like...
BACKGROUND
Anaerobes are normal flora of the human body. However, they can cause serious infections in humans. Anaerobic bacteria are known to cause respiratory infections like pneumonia and acute exacerbation of chronic lower airway infections. These are often missed due to the complexity of their isolation and identification. Hence, this study aimed to study anaerobes causing respiratory tract infections and determine their antibiotic susceptibility.
MATERIALS & METHODS
Clinical specimens such as bronchial aspirates and pleural aspirates collected from patients with respiratory diseases attending Vallabhbhai Patel Chest Institute were processed, the anaerobes isolated were identified, and their susceptibilities to various groups of antimicrobials were studied using standard microbiological methods.
RESULTS
Three hundred and fourteen patients were included in the study, 154 males and 160 females. Of these 314 patients, 148 (47%) yielded anaerobes in their clinical samples. Seventy patients had more than one type of anaerobic organism. Hence, 235 isolates were recovered belonging to as many as 17 genera. The MIC of seven antibiotics on 154 isolates was tested. The isolates belonged mostly to the genera Bacteroides, Prevotella, Veillonella, and Actinomyces. Variable resistance was observed to most classes of antibiotics by many genera.
CONCLUSIONS
Metronidazole is commonly used against anaerobes, but the study showed that the isolates were 20-30% resistant to the antibiotic. Starting this as an empirical therapy might lead to treatment failure.
Topics: Male; Female; Humans; Anti-Bacterial Agents; Bacteria, Anaerobic; Bacterial Infections; Microbial Sensitivity Tests; Drug Resistance, Bacterial; Anti-Infective Agents; Respiratory Tract Infections
PubMed: 37872502
DOI: 10.1186/s12866-023-03059-6 -
The ISME Journal Dec 2023The cycle of life and death and Earth's carbon cycle(s) are intimately linked, yet how bacterial cells, one of the largest pools of biomass on Earth, are recycled back...
The cycle of life and death and Earth's carbon cycle(s) are intimately linked, yet how bacterial cells, one of the largest pools of biomass on Earth, are recycled back into the carbon cycle remains enigmatic. In particular, no bacteria capable of scavenging dead cells in oxygen-depleted environments have been reported thus far. In this study, we discover the first anaerobes that scavenge dead cells and the two isolated strains use distinct strategies. Based on live-cell imaging, transmission electron microscopy, and hydrolytic enzyme assays, one strain (designated CYCD) relied on cell-to-cell contact and cell invagination for degrading dead food bacteria where as the other strain (MGCD) degraded dead food bacteria via excretion of lytic extracellular enzymes. Both strains could degrade dead cells of differing taxonomy (bacteria and archaea) and differing extents of cell damage, including those without artificially inflicted physical damage. In addition, both depended on symbiotic metabolic interactions for maximizing cell degradation, representing the first cultured syntrophic Bacteroidota. We collectively revealed multiple symbiotic bacterial decomposition routes of dead prokaryotic cells, providing novel insight into the last step of the carbon cycle.
Topics: Anaerobiosis; Bacteria; Bacteria, Anaerobic; Archaea; Environment
PubMed: 37872273
DOI: 10.1038/s41396-023-01538-2 -
Microbiome Aug 2023The interaction among microorganisms in the anaerobic digestion of food waste (ADFW) reactors lead to the degradation of organics and the recycling of energy. Viruses...
BACKGROUND
The interaction among microorganisms in the anaerobic digestion of food waste (ADFW) reactors lead to the degradation of organics and the recycling of energy. Viruses are an important component of the microorganisms involved in ADFW, but are rarely investigated. Furthermore, little is known about how viruses affect methanogenesis.
RESULTS
Thousands of viral sequences were recovered from five full-scale ADFW reactors. Gene-sharing networks indicated that the ADFW samples contained substantial numbers of unexplored anaerobic-specific viruses. Moreover, the viral communities in five full-scale reactors exhibited both commonalities and heterogeneities. The lab-scale dynamic analysis of typical ADFW scenarios suggested that the viruses had similar kinetic characteristics to their prokaryotic hosts. By associating with putative hosts, a majority of the bacteria and archaea phyla were found to be infected by viruses. Viruses may influence prokaryotic ecological niches, and thus methanogenesis, by infecting key functional microorganisms, such as sulfate-reducing bacteria (SRB), syntrophic acetate-oxidizing bacteria (SAOB), and methanogens. Metabolic predictions for the viruses suggested that they may collaborate with hosts at key steps of sulfur and long-chain fatty acid (LCFA) metabolism and could be involved in typical methanogenesis pathways to participate in methane production.
CONCLUSIONS
Our results expanded the diversity of viruses in ADFW systems and suggested two ways that viral manipulated ADFW biochemical processes. Video Abstract.
Topics: Anaerobiosis; Food; Refuse Disposal; Bacteria; Archaea; Methane; Bioreactors
PubMed: 37537690
DOI: 10.1186/s40168-023-01585-z -
Microbiology Spectrum Apr 2024Fluorescent proteins have revolutionized science since their discovery in 1962. They have enabled imaging experiments to decipher the function of proteins, cells, and...
Fluorescent proteins have revolutionized science since their discovery in 1962. They have enabled imaging experiments to decipher the function of proteins, cells, and organisms, as well as gene regulation. Green fluorescent protein and all its derivatives are now standard tools in cell biology, immunology, molecular biology, and microbiology laboratories around the world. A common feature of these proteins is their dioxygen (O)-dependent maturation allowing fluorescence, which precludes their use in anoxic contexts. In this work, we report the development and characterization of genetic circuits encoding the O-independent KOFP-7 protein, a flavin-binding fluorescent protein. We have optimized the genetic circuit for high bacterial fluorescence at population and single-cell level, implemented this circuit in various plasmids differing in host range, and quantified their fluorescence under both aerobic and anaerobic conditions. Finally, we showed that KOFP-7-based constructions can be used to produce fluorescing cells of , a facultative anaerobe, demonstrating the usefulness of the genetic circuits for various anaerobic bacteria. These genetic circuits can thus be modified at will, both to solve basic and applied research questions, opening a highway to shed light on the obscure anaerobic world.IMPORTANCEFluorescent proteins are used for decades, and have allowed major discoveries in biology in a wide variety of fields, and are used in environmental as well as clinical contexts. Green fluorescent protein (GFP) and all its derivatives share a common feature: they rely on the presence of dioxygen (O) for protein maturation and fluorescence. This dependency precludes their use in anoxic environments. Here, we constructed a series of genetic circuits allowing production of KOFP-7, an O-independant flavin-binding fluorescent protein. We demonstrated that cells producing KOFP-7 are fluorescent, both at the population and single-cell levels. Importantly, we showed that, unlike cells producing GFP, cells producing KOFP-7 are fluorescent in anoxia. Finally, we demonstrated that NS1, a facultative anaerobe, is fluorescent in the absence of O when KOFP-7 is produced. Altogether, the development of new genetic circuits allowing O-independent fluorescence will open new perspective to study anaerobic processes.
Topics: Green Fluorescent Proteins; Bacteria; Flavins; Oxygen; Vibrio
PubMed: 38441526
DOI: 10.1128/spectrum.04091-23 -
Advances in Clinical and Experimental... Aug 2023Refractory abdominal wounds are commonly complicated by surgical site infections, which prolong hospital stays and increase medical costs. There is little clinical data...
BACKGROUND
Refractory abdominal wounds are commonly complicated by surgical site infections, which prolong hospital stays and increase medical costs. There is little clinical data on the use of allogeneic platelet gel (PG) therapy for refractory infected wounds.
OBJECTIVES
This study aimed to evaluate the efficacy and safety of allogeneic PGs in the treatment of refractory abdominal wounds.
MATERIAL AND METHODS
A prospective single-center study was performed in a national abdominal trauma referral center between June 2019 and June 2021. A total of 11 patients with refractory abdominal wounds were treated with allogeneic PGs after the failure of standard medical treatments. The PGs were derived from platelets collected from healthy donors using apheresis, and each PG was tested for platelet count, transfusion-related diseases, aerobic and anaerobic bacteria, and growth factor concentration. Clinical efficacy was evaluated by assessing the wound surface and observing the condition of the wound, including wound area and percentage of granulation.
RESULTS
The median age of the patients was 37 years (1st quartile, 3rd quartile (Q1, Q3): 31-55 years), median (Q1, Q3) hemoglobin level was 95 g/L (78-120 g/L) and median (Q1, Q3) serum albumin level was 39.9 g/L (34.9-42.7 g/L). The PG platelet count was 976.5 ±174.9×109/L. Results of transfusion-associated contagion tests for aerobic and anaerobic bacteria were negative. Growth factor contents (pg/mL) were: for transforming growth factor beta 1 (TGF-β1); 2542.39 ±430.60, for platelet-derived growth factor BB (PDGF-BB); 23230.03 ±4236.14 and FOR vascular endothelial growth factor (VEGF); 91.41 ±23.31. The rate of wound healing was 100%, and the median (Q1, Q3) healing time was 30 days (18-40 days). The follow-up period was 5-27 months, during which no recurrence of the wounds was found.
CONCLUSIONS
The present study demonstrated that allogeneic PGs are a safe and effective treatment for refractory abdominal wounds.
Topics: Humans; Adult; Blood Platelets; Vascular Endothelial Growth Factor A; Prospective Studies; Wound Healing; Hematopoietic Stem Cell Transplantation
PubMed: 36753377
DOI: 10.17219/acem/159088 -
Gut Microbes 2024Antibiotic resistance is a global threat driven primarily by antibiotic use. We evaluated the effects of antibiotic exposures on the gut microbiomes and resistomes of...
Antibiotic resistance is a global threat driven primarily by antibiotic use. We evaluated the effects of antibiotic exposures on the gut microbiomes and resistomes of children at high risk of colonization by antibiotic-resistant bacteria. We performed shotgun metagenomic sequencing of 691 serially collected fecal samples from 80 children (<18 years) undergoing hematopoietic cell transplantation. We evaluated the effects of aerobic (cefepime, vancomycin, fluoroquinolones, aminoglycosides, macrolides, and trimethoprim-sulfamethoxazole) and anaerobic (piperacillin-tazobactam, carbapenems, metronidazole, and clindamycin) antibiotic exposures on the diversity and composition of the gut microbiome and resistome. We identified 372 unique antibiotic resistance genes (ARGs); the most frequent ARGs identified encode resistance to tetracyclines ( = 88), beta-lactams ( = 84), and fluoroquinolones ( = 79). Both aerobic and anaerobic antibiotic exposures were associated with a decrease in the number of bacterial species (aerobic, β = 0.71, 95% CI: 0.64, 0.79; anaerobic, β = 0.66, 95% CI: 0.53, 0.82) and the number of unique ARGs (aerobic, β = 0.81, 95% CI: 0.74, 0.90; anaerobic, β = 0.73, 95% CI: 0.61, 0.88) within the gut metagenome. However, only antibiotic regimens that included anaerobic activity were associated with an increase in acquisition of new ARGs (anaerobic, β = 1.50; 95% CI: 1.12, 2.01) and an increase in the relative abundance of ARGs in the gut resistome (anaerobic, β = 1.62; 95% CI: 1.15, 2.27). Specific antibiotic exposures were associated with distinct changes in the number and abundance of ARGs for individual antibiotic classes. Our findings detail the impact of antibiotics on the gut microbiome and resistome and demonstrate that anaerobic antibiotics are particularly likely to promote acquisition and expansion of antibiotic-resistant bacteria.
Topics: Child; Humans; Anti-Bacterial Agents; Bacteria; Fluoroquinolones; Gastrointestinal Microbiome; Hematopoietic Stem Cell Transplantation
PubMed: 38555499
DOI: 10.1080/19490976.2024.2333748 -
Heliyon Sep 2023Sewage sludge (SS) is an environmental issue due to its high organic content and ability to release hazardous substances. Most of the treatments available are... (Review)
Review
Sewage sludge (SS) is an environmental issue due to its high organic content and ability to release hazardous substances. Most of the treatments available are biological, thermal hydrolysis, mechanical (ultrasound, high pressure, and lysis), chemical with oxidation (mainly ozonation), and alkali pre-treatments. Other treatment methods include landfill, wet oxidation, composting, drying, stabilization, incineration, pyrolysis, carbonization, liquefaction, gasification, and torrefaction. Some of these SS disposal methods damage the ecosystem and underutilize the potential resource value of SS. These challenges must be overcome with an innovative technique for the improvement of SS's nutritional value, energy content, and usability. This review proposes plasma pyrolysis and anaerobic digestion (AD) as promising SS treatment technologies. Plasma pyrolysis pre-treats SS to make it digestible by AD bacteria and immobilizes the heavy metals. The addition of Char to the upstream AD process increases the quantity and quality of biogas produced while enhancing the nutrients in the digestate. These two processes are integrated at high temperatures, thus creating concerns about their energy demand. These challenges are offset by the generated energy that can run the treatment plant or be sold to the grid, generating additional cash. Plasma pyrolysis wastes can also be converted into biochar, organic fertilizer, or soil conditioner. These combined technologies' financial sustainability depends on the treatment facility's circumstances and location. Plasma pyrolysis and AD can treat SS sustainably and provide nutrients and resources. This paper explains the co-process treatment route's techno-economic prospects, challenges, and recommendations for the future application of SS valorization and resource recovery.
PubMed: 37809742
DOI: 10.1016/j.heliyon.2023.e19765 -
Integrated microalgae-bacteria modelling: application to an outdoor membrane photobioreactor (MPBR).The Science of the Total Environment Aug 2023A mechanistic model describing the key interactions occurring in microalgae-bacteria consortia systems was developed and validated. The proposed model includes the most...
A mechanistic model describing the key interactions occurring in microalgae-bacteria consortia systems was developed and validated. The proposed model includes the most relevant features of microalgae, such as light dependence, endogenous respiration, growth, and nutrient consumption for different nutrient sources. The model is coupled to the plant-wide model BNRM2, including heterotrophic and nitrifying bacteria, and chemical precipitation processes, among others. A major novelty of the model is microalgae growth inhibition by nitrite. Validation was conducted using experimental data from a pilot-scale membrane photobioreactor (MPBR) fed with permeate from an anaerobic membrane bioreactor (AnMBR). Three experimental periods dealing with different interactions between nitrifying bacteria and microalgae were validated. The model was able to accurately represent the dynamics occurring in the MPBR, predicting the relative abundance of microalgae and bacteria over time. Specifically, >500 pairs of experimental and modeled data were evaluated, giving an average R coefficient of 0.9902. The validated model was also used to evaluate different offline control strategies for enhancing process performance. For example, partial-nitrification resulting in NO-N accumulation (i.e., microalgae growth inhibition) could be avoided by increasing biomass retention time from 2.0 to 4.5 days. It has been also concluded that microalgae biomass growth rate could be also enhanced by punctually increasing the dilution rate, allowing to outcompete nitrifying bacteria.
Topics: Photobioreactors; Microalgae; Wastewater; Bacteria; Biomass
PubMed: 37149200
DOI: 10.1016/j.scitotenv.2023.163669 -
Biotechnology For Biofuels and... Aug 2023Feed shortage is an important factor limiting livestock production in the world. To effectively utilize natural woody plant resources, we used wilting and microbial...
BACKGROUND
Feed shortage is an important factor limiting livestock production in the world. To effectively utilize natural woody plant resources, we used wilting and microbial additives to prepare an anaerobic fermentation feed of mulberry, and used PacBio single-molecule real-time (SMRT) sequencing technology to analyse the "enzyme-bacteria synergy" and fermentation mechanism.
RESULTS
The fresh branches and leaves of mulberry have high levels of moisture and nutrients, and also contain a diverse range of epiphytic microorganisms. After ensiling, the microbial diversity decreased markedly, and the dominant bacteria rapidly shifted from Gram-negative Proteobacteria to Gram-positive Firmicutes. Lactic acid bacteria (LAB) emerged as the dominant microbial population, resulting in increased in the proportion of the carbohydrate metabolism and decreased in the proportion of the amino acid and "global and overview map" (GOM) metabolism categories. The combination of cellulase and LAB exhibited a synergistic effect, through which cellulases such as glycanase, pectinase, and carboxymethyl cellulase decomposed cellulose and hemicellulose into sugars. LAB converted these sugars into lactic acid through the glycolytic pathway, thereby improving the microbial community structure, metabolism and fermentation quality of mulberry silage. The GOM, carbohydrate metabolism, and amino acid metabolism were the main microbial metabolic categories during ensiling. The presence of LAB had an important effect on the microbial community and metabolic pathways during silage fermentation. A "co-occurrence microbial network" formed with LAB, effectively inhibiting the growth of harmful microorganisms, and dominating the anaerobic fermentation process.
CONCLUSIONS
In summary, PacBio SMRT was used to accurately analyse the microbial network information and regulatory mechanism of anaerobic fermentation, which provided a scientific basis for the study of woody silage fermentation theory. This study reveals for the first time the main principle of the enzyme-bacteria synergy in a woody silage fermentation system, which provides technical support for the development and utilization of woody feed resources, and achieves sustainable livestock production.
PubMed: 37542284
DOI: 10.1186/s13068-023-02368-2 -
Journal of Clinical Medicine Jul 2023The aim of the study was to compare the prevalence of the nasopharyngeal carriage of culturable microorganisms in the microbiota of asymptomatic women with a...
The aim of the study was to compare the prevalence of the nasopharyngeal carriage of culturable microorganisms in the microbiota of asymptomatic women with a physiological pregnancy (PW) and nonpregnant women (NPW). Nasopharyngeal swabs were collected from 53 PW and 30 NPW to detect bacterial and fungal colonization. Isolates were identified using the culture method and the MALDI-TOF MS technique. The nasopharyngeal microbiota (NPM) partially differed between PW and NPW. These differences in the frequency of nasopharyngeal colonization between the PW and NPW groups were not statistically significant ( > 0.05); all cases were colonized by bacteria and only two cases in the PW group were colonized by yeasts, namely, spp. High levels of staphylococcal colonization, including predominantly coagulase-negative staphylococci and in the nasopharyngeal sample, were present in both groups. The reduced number of Gram-negative rods colonized in the cases studied was seen in samples from the NPW group, particularly with , and anaerobic spp. were isolated only in the PW group ( < 0.05). Moreover, a higher carriage rate of colonization was statistically significant ( < 0.05) and correlated with the NPW group. Pregnancy may disturb the composition of the NPM represented by commensals and opportunistic bacteria and promote yeast colonization as compared to nonpregnant women.
PubMed: 37445482
DOI: 10.3390/jcm12134447