Bacterial Populations Research Articles

Antimicrobial effects of pulsed light activated TiO2-Polylactic acid film

A study was conducted to evaluate the antimicrobial effect of TiO2 incorporated polylactic acid (PLA) films, activated by pulsed light (PL). TiO2-PLA films with 0, 0.5, 5, 10, and 20 % TiO2/PLA ratio were developed by the solvent casting method. Populations of Escherichia coli and Listeria on film surfaces were determined after the films were PL-treated in three ways: PL treatment on the inoculated film surface; PL treatment from the reverse side of the inoculated film surface; PL treatment before the inoculation on the film surface. A 5 s PL treatment reduced E. coli populations on PLA film from 6.2 to 2.5 log CFU/cm2 and on TiO2-PLA film from 6.2 to 1.1 log CFU/cm2, indicating the combined antibacterial effect of PL and TiO2. Light-activated TiO2-PLA films maintained antibacterial activity against E. coli and L. innocua for 2 h after the 5 s PL treatment, as the activated TiO2-PLA films were still able to reduce bacterial populations by up to 2.5 log CFU/cm2. These findings suggest that pre-activated TiO2-PLA films have potential for packaging foods that are sensitive to UV light.

Modelling the influence of vitamin D and probiotic supplementation on the microbiome and immune response

Abstract The intestinal microbiota play a critical role in human health and disease, maintaining metabolic and immune/inflammatory health, synthesizing essential vitamins and amino acids and maintaining intestinal barrier integrity. The aim of this paper is to develop a mathematical model to describe the complex interactions between the microbiota, vitamin D/vitamin D receptor (VDR) pathway, epithelial barrier and immune response in order to understand better the effects of supplementation with probiotics and vitamin D. This is motivated by emerging data indicating the beneficial effects of vitamin D and probiotics individually and when combined. We propose a system of ordinary differential equations determining the time evolution of intestinal bacterial populations, concentration of the VDR:1,25(OH)$_{2}$D complex in epithelial and immune cells, the epithelial barrier and the immune response. The model shows that administration of probiotics and/or vitamin D upregulates the VDR complex, which enhances barrier function and protects against intestinal inflammation. The model also suggests co-supplementation to be superior to individual supplements. We explore the effects of inflammation on the populations of commensal and pathogenic bacteria and the vitamin D/VDR pathway and discuss the value of gathering additional experimental data motivated by the modelling insights.

Cadmium (Cd) detoxification and activation of plant defense enzymes activation in Wheat (Triticum aestivum) through the use of endophytic Bacillus thuringiensis and Salix alba root powder

Cadmium (Cd) is a toxic heavy metal and a threat to the ecosystem therefore the current investigation was designed to use endophytic bacteria from the Salix alba roots and to investigate its plant growth promoting and Cd detoxification ability with and without Salix alba root powder. In a complete randomized design (CRD), the cadmium sulfate was applied at the rate of 20mg/kg and 40mg/kg soil. The Bacillus thuringiensis (Accession # MW979616) was identified from Salix alba roots. The combination of Bacillus thuringiensis inoculated seeds +0.5gm root powder showed significant increase in wheat shoot dry weight, root fresh weight, catalase, and ascorbate peroxidases by 457%, 223%, 105% and 74%, respectively. The application of Bacillus thuringiensis with Salix alba root powder boosted the plant growth and defense at higher concentrations of Cd. In another treatment with Bacillus thuringiensis inoculated seeds + CdSO4 40mg/kg + 0.5gm root powder significantly increased the shoot fresh weight, root fresh weight, root dry weight, proline, sugar, superoxide dismutase, and peroxidase by 456%, 650%, 115%, 91%, 80%, 350%, and 250%, respectively with 80% reduction in plant Cd accumulation and increased bacterial population. Bacillus thuringiensis and Salix alba root powder can be useful for plant growth, Cd toxicity mitigation, accelerating bacterial activity in Cd-contaminated soil and uplifting the plant defense under heavy metal stress.

Influence of phosphate and potassium solubilizing bacteria on performance of crop, endophytic and rhizosphere microbial population in chamomile

Phosphate (Bacillus megaterium) and potassium (Frateuria aurantia) solubilizing bacteria (PSB and KSB) were assessed for their agronomic impact on chamomile performance in a pot experiment at CSIR-CIMAPRC, Bengaluru. Results demonstrated that 75% recommended dose of fertilizer (RDF) combined with PSB and KSB significantly improved chamomile performance, enhancing plant height (41.4 cm), stem diameter (1.10 mm), number of flowers (348.67), flower: leaf ratio (1.24), and flower dry weight (4.28 g plant-1) compared to control, RDF alone, and sole solubilizer application. The combined application with 100% RDF synergistically increased rhizosphere bacterial population from 25 × 104 Cfu g-1 to 57 × 104 cfu g-1, while 75% RDF + PSB + KSB resulted in 53 × 104 cfu g-1. Morphological and biochemical analyses revealed diverse variations in chamomile endophytes and rhizosphere soil bacterial populations, mainly Bacillus and Streptococcus genera. PSB and KSB, whether applied individually or combined, significantly influenced chamomile growth and yield, with microbial dynamics enhancing nutrient solubilization and availability.

Contribution of the Mobilome to the Configuration of the Resistome of Corynebacterium striatum

Corynebacterium striatum, present in the microbiota of human skin and nasal mucosa, has recently emerged as a causative agent of hospital-acquired infections, notable for its resistance to multiple antimicrobials. Its mobilome comprises several mobile genetic elements, such as plasmids, transposons, insertion sequences and integrons, which contribute to the acquisition of antimicrobial resistance genes. This study analyzes the contribution of the C. striatum mobilome in the transfer and dissemination of resistance genes. In addition, integrative and conjugative elements (ICEs), essential in the dissemination of resistance genes between bacterial populations, whose role in C. striatum has not yet been studied, are examined. This study examined 365 C. striatum genomes obtained from the NCBI Pathogen Detection database. Phylogenetic and pangenome analyses were performed, the resistance profile of the bacterium was recognized, and mobile elements, including putative ICE, were detected. Bioinformatic analyses identified 20 antimicrobial resistance genes in this species, with the Ermx gene being the most predominant. Resistance genes were mainly associated with plasmid sequence regions and class 1 integrons. Although an ICE was detected, no resistance genes linked to this element were found. This study provided valuable information on the geographic spread and prevalence of outbreaks observed through phylogenetic and pangenome analyses, along with identifying antimicrobial resistance genes and mobile genetic elements that carry many of the resistance genes and may be the subject of future research and therapeutic approaches.

Safety Evaluation and antioxidant potential of new probiotic strain Bacillus subtilis (NMCC-path-14) in Balb/c mice by sub-acute repeated dose toxicity

Probiotics have recently gained significant interest for their possible therapeutic effects in treating numerous health conditions. Probiotics containing Bacillus subtilis have been shown to have several health benefits, most notably in preventing diarrhea and gastrointestinal problems. A novel probiotic strain, Bacillus subtilis (NMCC-path-14), isolated from the rumen of a Nilli Ravi Buffalo, was evaluated for 28-day repeated dose toxicity in Balb/c mice. The NMCC-path-14 in low dose (1 × 108 CFU/ml) and high dose (1 × 1010 CFU/ml) was administered to the mice through gavage regularly. After 28 days of treatment, it was discovered that the no-observed-adverse-effect level (NOAEL) for NMCC-path-14 wasgreater than 1 × 1010 CFU/animal/day. This study also revealed no treatment-related changes in clinical parameters, body weight, gross pathology, or histology. Food consumption, hemoglobin, hematocrit, red blood cell counts, and colon length increased, while total/differential leukocyte count and platelets remained unchanged. The administration of NMCC-path-14 also resulted in decreased bilirubin and creatinine levels. Furthermore, NMCC-path-14 also displayed a promising antioxidant potential by increasing the antioxidant enzymes (GST, GSH, and CAT) and decreasing oxidant enzyme (MDA and NO) levels in vital organs like the liver, kidneys, spleen, and colon. TheNMCC-path-14also decreased the pathogenic bacterial population while increasing the beneficial population. Given the lack of adverse effects observed after NMCC-path-14 treatment, this strain is safe and must be considered as a potential probiotic in humans.

Intragenic DNA inversions expand bacterial coding capacity.

Bacterial populations that originate from a single bacterium are not strictly clonal and often contain subgroups with distinct phenotypes1. Bacteria can generate heterogeneity through phase variation-a preprogrammed, reversible mechanism that alters gene expression levels across a population1. One well-studied type of phase variation involves enzyme-mediated inversion of specific regions of genomic DNA2. Frequently, these DNA inversions flip the orientation of promoters, turning transcription of adjacent coding regions on or off2. Through this mechanism, inversion can affect fitness, survival or group dynamics3,4.Here, we describe the development of PhaVa, a computational tool that identifies DNA inversions using long-read datasets.We alsoidentify 372 'intragenic invertons', a novel class of DNA inversions found entirely within genes, in genomes of bacterial and archaeal isolates. Intragenic invertons allow a gene to encode two or more versions of a protein by flipping a DNA sequence within the coding region, thereby increasing coding capacity without increasing genome size. We validate ten intragenic invertons in the gut commensal Bacteroides thetaiotaomicron, and experimentally characterize an intragenic inverton in the thiamine biosynthesis gene thiC.

Influence of a synthetic analogue of the active center of GM-CSF – peptide ZP2 on the growth and biofilm formation of gram-negative bacteria – causes of surgical infections

The aim is to analyze the nature of the effect of the synthetic analogue of the active center of GM- CSF – peptide ZP2 on the growth and biofilm formation (BPO) of gram–negative bacteria – pathogens of surgical infections. The study used 18 clinical isolates of gram-negative bacteria of different species (Klebsiella pneumoniae, Citrobacter freundii, Stenotrophamonas maltophilia) isolated from purulent wounds in patients with surgical pathology and showing pronounced resistance to many antibiotics used in clinical practice. The isolation of pure cultures of microorganisms was carried out by conventional methods; species were assessed by direct protein profiling using a MALDI TOF mass spectrometer. To study the effect of ZP2 peptide on bacterial growth and BPO, isolates were co-cultured with a solution of ZP2 peptide in meat-peptone broth (MPB) at a concentration of 5 micrograms/ml at 37°C for 24-48 hours. The effect of the ZP2 peptide was studied both on emerging biofilms and on those formed, according to the degree of binding of crystalline violet in sterile 96-well polystyrene plates. Next, Growth inhibition indices and coefficients of BPO of microorganisms were determined. It was found that the synthetic analogue of the active center of granulocyte-macrophage colony stimulating factor (GM-CSF) – peptide ZP2 inhibited the growth of the studied bacterial strains, reducing the biomass of experimental cultures during the development of bacterial populations. At the same time, the species-specific effect of the ZP2 peptide on the ability of surgical strains of the studied bacteria to form biofilms has been shown. It was experimentally established that all the studied surgical strains of microorganisms were capable of biofilm formation, and the maximum severity of the trait was characteristic of S. maltophilia isolates. The synthetic analogue of the active center of granulocyte-macrophage colony stimulating factor (GM-CSF) – peptide ZP2 caused a decrease in the ability to form biofilms in isolates S. maltophilia and destroyed already formed biofilms in all studied species of microorganisms. The experimental data obtained expand the range of potential clinical applications of the synthetic analogue of the active center of granulocyte-macrophage colony stimulating factor (GM-CSF) – peptide ZP2, and its use in new medicines can be effective in combating antibiotic-resistant pathogens of surgical infections.

Application of hsp60 amplicon sequencing to characterize microbial communities associated with juvenile and adult Euprymna scolopes squid.

The symbiotic relationship between Vibrio (Aliivibrio) fischeri and the Hawaiian bobtail squid, Euprymna scolopes, serves as a key model for understanding host-microbe interactions. Traditional culture-based methods have primarily isolated V. fischeri from the light organs of wild-caught squid, yet culture-independent analyses of this symbiotic microbiome remain limited. This study aims to enhance species-level resolution of bacterial communities associated with E. scolopes using hsp60 amplicon sequencing. We validated our hsp60 sequencing approach using pure cultures and mixed bacterial populations, demonstrating its ability to distinguish V. fischeri from other closely-related vibrios and the possibility of using this approach for strain-level diversity with further optimization. This approach was applied to whole-animal juvenile squid exposed to either seawater or a clonal V. fischeri inoculum, as well as ventate samples and light organ cores from wild-caught adults. V. fischeri accounted for the majority of the identifiable taxa for whole-animal juvenile samples and comprised 94%-99% of amplicon sequence variants (ASVs) for adult light organ core samples, confirming that V. fischeri is the dominant, if not sole, symbiont typically associated with E. scolopes light organs. In one ventate sample, V. fischeri comprised 82% of reads, indicating the potential for non-invasive community assessments using this approach. Analysis of non-V. fischeri ASVs revealed that Bradyrhizobium spp. and other members of the Rhodobacterales order are conserved across juvenile and adult samples. These findings provide insight into the presence of additional microbial associations with the squid host tissue outside of the light organ that have not been previously detected through traditional culture methods.

Antibacterial and therapeutic potential of historic deposits of silesian healing clay – terra sigillataSilesiaca

Ethnopharmacological relevanceThe increasing evolution of pathogen resistance is a global problem that requires novel solutions. Recently, an increased interest in ethnomedicinal sources can be observed in the derivation of new medicines. The return to traditional medicinal formulations handed down for generations is being followed, but it is necessary to revise them again, taking into account the generally accepted research protocol. Aim of the studyWe aimed to evaluate the antimicrobial potential of historical deposits of Silesian healing clay (SHC), used in ethnomedicine against Gram-positive bacteria and to assess their biological activity using a primary dermal fibroblast line (NHDF) and a model monocyte line (THP1). Materials and methodsInformation on medicinal clay deposits that occur in Silesia and are traditionally used in ethnomedicine or ancient medicine and known as terra sigillata Silesiaca or SHC, was selected on available source materials and old prints and maps from the archives of the Polish Geological Institute (Wrocław, Poland). Subsequently, their places of occurrence were identified and traced in the field by taking three deposits from the Silesia territory: Upper Silesia (D1), Opole Silesia (D2), and Lower Silesian (D3) Voivodeships for analysis. Their basic parameters and antimicrobial efficacy against pathogenic bacteria, Gram-positive streptococci and staphylococci, including methicillin-resistant strains, were examined. The study evaluated the effects of clays on growth and vitality using a primary dermal fibroblast line (NHDF) and a monocytic line (THP1). Studies were performed on a cell culture model to determine the effects on tissue regeneration (fibroblasts) and anti-inflammatory effects (monocytes). The study attempted to identify the mechanism of antimicrobial action, especially the textural characteristics and geochemical composition, as well as the environmental reaction (pH). ResultsSHCs were classified into the following textural classes: clay loam (D1), clay (D2), and sand (D3). The tested deposits have antimicrobial properties that reduce the bacterial population (104 CFU) compared to the control (108 CFU). The antimicrobial effect depends on the type of clay and the species or strain of bacteria used. In-house studies clearly showed that Staphylococcus aureus Pcm 2054 and Staphylococcus epidermidis MRSE ATCC 2538 cells were completely adsorbed by clay minerals from clay D3.13. Furthermore, 10% leachates also showed an antimicrobial effect, as a reduction in bacterial populations was observed ranging from 91 to 100%. The results showed stimulation of fibroblast culture proliferation and inhibition of the growth of inflammatory cells (monocytes). ConclusionSHCs tested have antimicrobial potential, in particular D2.7, D2.11, and D3.13. The D3.13 deposit had a bactericidal effect against the staphylococci tested. Aqueous solutions of clays also showed bacteriostatic effect. The results obtained in cell culture model tests indicate properties that modulate the healing process – stimulation of fibroblast growth (NHDF line) and inhibition of monocyte growth (THP1 line).

The impact of Codonopsis Pilosulae and Astragalus Membranaceus extract on growth performance, immunity function, antioxidant capacity and intestinal development of weaned piglets.

The objective of this study was to examine the impact of Codonopsis pilosula and Astragalus membranaceus extract (CA) on the growth performance, diarrhea rate, immune function, antioxidant capacity, gut microbiota, and short-chain fatty acids (SCFAs) in weaned piglets. A total of forty-eight 31-day-old weaned piglets, were divided into four groups randomly based on the treatment type: control group (CON), low dose group (LCA, 0.5% CA), medium dose group (MCA, 1.0% CA), and high dose group (HCA, 1.5% CA), and were fed for a duration of 28 days. On the morning of the 1st and 29th day, the piglets were assessed by weighing them on an empty stomach, recording their daily feed intake and diarrhea rate. CA increased the average daily weight gain and reduced F/G without significant differences, and the diarrhea rate was reduced in the LCA and MCA groups. Furthermore, the levels of T-AOC, SOD, GSH-Px, and MDA were increased. The levels of T-AOC in the LCA group and the MCA group, SOD in the MCA group, and GSH-Px in the HCA group were significantly higher compared with the CON group (p < 0.05). Additionally, CA significantly increased IgM, IgG, and IgA levels (p < 0.05). The results of gut microbiota analysis showed that the bacterial population and diversity of faeces were changed with the addition of CA to basal diets. CA increased the abundance of the beneficial bacterial Firmicutes and Lactobacillus. Additionally, Compared with the CON group, CA significantly increased the SCFAs content of weaned piglets (p < 0.05). CA can alleviate oxidative stress, improve immunity and antioxidant capacity, increase the abundance of beneficial bacteria, and the content of SCFAs for improving the intestinal barrier of piglets, thus promoting growth and reducing diarrhea rate in weaned piglets.

Efficacy of zinc nanoparticle supplementation on ruminal environment in lambs

BackgroundZinc nanoparticles (NPs) are characterized by high bioavailability, small size, and high absorbability. The purpose of this experiment was to determine the effect of Zn-NP feed supplementation on ruminal fermentation, microbiota, and histopathology in lambs. In vitro (24 h), short-term (STE, 28 d), and long-term (LTE, 70 d) experiments were performed. The lambs in STE were fed a basal diet (BD) composed of 350 g/d ground barley and 700 g/d meadow hay (Control), BD enriched with ZnO-NPs (80 mg Zn/kg of diet, ZnO-NPs), and BD enriched with Zn phosphate-based NPs (80 mg Zn/kg of diet, ZnP-NP). The in vitro gas production technique was used in incubated rumen fluid from STE. The lambs in LTE were fed BD (Control), BD enriched with ZnO-NPs (40 mg Zn/kg of diet, ZnO-NP40), BD enriched with ZnO-NPs (80 mg Zn/kg of diet, ZnO-NP80) and BD enriched with ZnO (80 mg Zn/kg of diet, ZnO-80).ResultsAfter 24 h of incubation, dry matter digestibility was higher for ZnO-NP and ZnP-NP substrates than the control in an in vitro experiment (P < 0.001). The total bacterial population in the STE was lower (P < 0.001) in the ZnP-NP group than in the control and ZnO-NP groups, but the protozoan populations were not significantly different. The ammonia-N concentration in LTE was lowest in the ZnO-NP80 group (P = 0.002), but the activities of carboxymethyl cellulase (P < 0.001) and xylanase (P = 0.002) were higher in the ZnO-NP40, ZnO-NP80, and ZnO-80 groups than in the control group. Morphological observation after STE and LTE revealed histological changes (e.g. inflammation of the epithelium or edema of the connective tissue) in the rumen of lambs.ConclusionZn-NP supplementation up to 70 d improved feed-use efficiency and influenced ammonia-N concentration and activities of hydrolases in the rumen. The active ruminal fermentation affected the health of the ruminal papillae and epithelium in the lambs, regardless of the application's form, dose, or duration. However, by affecting rumen microbial fermentation, Zn-NPs could alter fermentation patterns, thereby increasing the capacity of host rumen epithelial cells to transport short-chain fatty acids.

Specialized Listeria monocytogenes produce tailocins to provide a population-level competitive growth advantage.

Tailocins are phage tail-like bacteriocins produced by various bacterial species to kill kin competitors. Given that tailocin release is dependent upon cell lysis, regulation of tailocin production at the single-cell and population level remains unclear. Here we used flow cytometry, competition assays and structural characterization of tailocin production in a human bacterial pathogen, Listeria monocytogenes. We revealed that a specialized subpopulation, constituting less than 1% of the total bacterial population, differentiates to produce, assemble and store thousands of tailocin particles. Tailocins are packed in a highly ordered manner, clustered in a liquid crystalline phase that occupies a substantial volume of the cell. Tailocin production confers a competitive growth advantage for the rest of the population. This study provides molecular insights into tailocin production as a form of altruism, showing how cell specialization within bacterial populations can confer competitive advantages at the population level.

Evolution of bacterial flora in raw yak milk and its effect on quality characteristics during frozen storage

Due to the scarcity of yak milk in Tibetan areas, local herders primarily use traditional freezing methods for preservation. However, the extent of microbial contamination in raw yak milk during frozen storage and its impact on milk quality remains largely unexplored. This study analyzed the changes in bacterial populations and quality of raw yak milk stored at −18 °C for 6 months. The results indicated that, compared to fresh milk, the freshness of yak milk showed no significant change after 2 months of frozen storage (P > 0.05). After 4 months, the bacterial diversity of flora in yak milk increased significantly, with Pseudomonas and Acinetobacter emerging as the dominant psychrophilic bacteria. Correspondingly, the expression of metabolic pathways related to quality deterioration increased, with a significant increase in physicochemical indicators such as acidity, proteolysis degree, acid value and fat oxidation degree (P < 0.05). Extending the frozen storage to 6 months resulted in a slight but no significant decrease in bacterial diversity, with no significant difference in quality deterioration compared to the 4-month group (P > 0.05). Correlation analysis further revealed that Acinetobacter and Psychrobacter were significantly positively correlated with quality deterioration of frozen milk (P < 0.05). In summary, when frozen for more than 4 months, raw yak milk exhibited the highest bacterial diversity and predicted the most abundant metabolic pathways, with dominant psychrophilic bacteria massive proliferation leading to a decline in quality and safety.

Role of organic amendments in improving the morphophysiology and soil quality of Setaria italica under salinity

Salinity negatively impacts soil fertility by impairing the development and physiological functions of foxtail millet plants. Organic amendments have emerged as a viable solution in the reclamation and management of salinity inflicted soils and improve the performance of crop. In this regard, a pot experiment was carried out to examine the effect of organic amendments (OAs) on soil quality and its influence on the growth and physiology of foxtail millet under saline and non-saline condition. The findings indicated that under salt stress conditions, the levels of proline, hydrogen peroxide (H2O2), and electrolyte leakage (EL) risen, whilst other physiological parameters decrease in foxtail millet. However, the addition of OAs, particularly dhaincha and biochar (BC), has shown a promising salt tolerant amendment among others. Its addition improved the growth performance of salinity-stressed plants, including plant height, fresh and dry biomass, simultaneously decreased sodium ion (Na+) and improved calcium (Ca2+), potassium (K+), and nitrate ion (NO3−). They also increased proline build up by 6–17 %, reduced H2O2 (19–38 %) and malondialdehyde (16–18 %). Furthermore, they elevated the relative water content (RWC) (25 %), chlorophyll content, and reduced EL (29–50 %). Once more, dhaincha and BC enhanced the number of rhizobia, phosphorus-solubilizing bacteria (PSB) and overall bacterial population in the soil. In saline soil, daincha and BC could enhance soil organic matter (628 %), total nitrogen (1630 %), available phosphorus (32–38 %), and exchangeable potassium (54–73 %). A potential strategy for improving setaria italica performance under salt is suggested to be the following order, dhaincha > biochar > vermicompost > duckweed. The study would assist stakeholders in these salinity-prone areas in strategizing the use of OAs to their fallow land for cultivation and agricultural activities.

Comparison of Different DNA Sampling and Extraction Protocols for Bacterial and Archaeal Populations Analysis in Water Buffalo

Methane (CH4) is a potent greenhouse gas, and ruminants are a significant source of agricultural emissions. It has been hypothesized that the host's genome controls rumen microbial communities, but robust results require numerous samples. The feasibility of a research project will depend on the ease and representativeness of the sampling method, as well as the cost-efficiency of large-scale sequencing. This study aimed to compare different protocols to investigate whether non-invasive samples could serve as a substitute for ruminal digesta. DNA recovery was tested in various matrices (whole rumen content, feces, and buccal swabs) from five cannulated buffalo cows. Three types of buccal swabs were tested, as well as feces in different forms (as-is, pelleted, or in a glycerol solution) and the rumen content. The study compared different protocols for DNA extraction, including WUR protocol, Maxwell®, and Quick Extract™, and two sampling times. Saliva was a challenging matrix to process, obtaining unsatisfactory DNA yield. Feces showed higher yields when pelleted but lower than rumen. The highest amount of DNA was obtained from whole rumen content using all three DNA extraction methods. Quick Extract was the easiest method to perform, while WUR resulted in the highest yield of DNA, swabs excluded. The Maxwell® method gave satisfactory results with all three matrices. However, further metagenomic analysis is required to verify if the species composition is comparable.

Metagenomic Analysis during Co-Digestion Buffalo Sludge and Tomato Pomace Post Thermal Stress: A Case Study

The tomato industry and buffalo farming generate waste, including sludge (BS) and tomato pomace (TP), which can significantly impact their economic and environmental sustainability. The case study tracked changes in microflora composition after a thermal shock during anaerobic co-digestion. The inoculum-to-substrate ratio was 0.5 based on volatile solid content under mesophilic conditions. An Automatic Methane Potential Test System was used to monitor the process before and after thermal stress (50°C) occurred for three days. Next-generation sequencing analyzed the bacterial and archaeal communities. The pH decreased, and methane production plateaued due to the high volatile solid content (87 g/L). After thermal stress, the pH returned to neutral, and the batch resumed biogas production. The cumulative CH4 production reached 3,115 Nml. The biogas had a maximum methane peak of 78.5% compared to 58.4% in BS. The taxonomic classification showed that Firmicutes (51.7%) and Bacteroidetes (29.9%) represented 81.6% of the total OTUs among the bacteria. Fonticella, the most abundant Clostridiaceae (average 4.3%), was absent in BS and increased (up to 17.1%) in TP during methane production. Methanocorpusculum was the most abundant in the archaeal community. However, Metanosarcina showed a stronger correlation with methane production. Brief thermal stress significantly altered bacterial and archaeal populations and allowed to resume biogas production.

RNA Sequencing of Sperm from Healthy Cattle and Horses Reveals the Presence of a Large Bacterial Population.

RNA molecules within ejaculated sperm can be characterized through whole-transcriptome sequencing, enabling the identification of pivotal transcripts that may influence reproductive success. However, the profiling of sperm transcriptomes through next-generation sequencing has several limitations impairing the identification of functional transcripts. In this study, we explored the nature of the RNA sequences present in the sperm transcriptome of two livestock species, cattle and horses, using RNA sequencing (RNA-seq) technology. Through processing of transcriptomic data derived from bovine and equine sperm cell preparations, low mapping rates to the reference genomes were observed, mainly attributed to the presence of ribosomal RNA and bacteria in sperm samples, which led to a reduced sequencing depth of RNAs of interest. To explore the presence of bacteria, we aligned the unmapped reads to a complete database of bacterial genomes and identified bacteria-associated transcripts which were characterized. This analysis examines the limitations associated with sperm transcriptome profiling by reporting the nature of the RNA sequences among which bacterial RNA was found. These findings can aid researchers in understanding spermatozoal RNA-seq data and pave the way for the identification of molecular markers of sperm performance.

On a Steady-State Probability Distribution for the Bacterial Population Growth Under the Impact of Antimicrobial Resistance and its Properties

On a Steady-State Probability Distribution for the Bacterial Population Growth Under the Impact of Antimicrobial Resistance and its Properties

Impact of neutrophil‐activating protein conservation on diagnostic tests and vaccine design

AbstractBACKGROUNDThe neutrophil activating protein (NAP) is a highly immunogenic and virulence factor of Helicobacter pylori, presenting inflammatory and immunomodulatory activity. Consequently, NAP has been explored as a diagnostic and therapeutic target. However, when evaluating a target protein to design diagnostic methods or vaccines, it is critical to determine the protein conservation among the bacterial population, as well the impact of alterations of amino acid residues on the protein antigenic profile.RESULTSIn the present work, NAP conservation and theoretical antigenicity were determined among 51 sequences from H. pylori isolated from patients worldwide. A high NAP conservation (83%) was observed, where 17 amino acid residues, among the 144 residues of the protein, were polymorphic. Alterations at these polymorphic sites had a theoretically low impact on predicted antigenicity, where only 5 NAPs out of 51 NAPs presented a slightly different antigenic profile in relation to the consensus sequence. According to that, it was possible to recognize in western blotting 93% of NAP from different bacteria (n = 15) using polyclonal antibodies developed against a specific NAP.CONCLUSIONSIt was predicted that when working with polyclonal antibodies or large NAP fragments for diagnostic and vaccine design, slight variation in protein sequence will have a minimal impact on NAP recognition. However, if a NAP monoclonal antibody or small NAP epitopes are considered, it is critical to select the most conserved and antigenic NAP regions, to maximize the coverage of NAP variants. © 2024 Society of Chemical Industry (SCI).