Distribution Of Bacterial Species Research Articles

Bioleaching of low-grade copper sulfide enhanced by nutrients from sterilized medical waste

Medical waste (MW) is originated from healthcare activities, which is difficult to dispose and potential to cause environmental pollution. The effect of MW on bioleaching of low-grade copper sulfide ore was studied, which showed that using MW can improve copper recovery through decreasing Fe3+ concentration and facilitating mutual conversion between Fe2+ and Fe3+. An appropriate-dosage MW improved bacterial concentration and attached bacteria proportion, while excessive MW caused harm to bacterial community structure succession. Using MW contributed the conversion from Fe3+ to Fe2+ to impede Fe3+ hydrolysis, thus diminishing the formation of passivation layer and augmenting copper recovery. The optimal distribution of bacterial species and maximum copper recovery of 82.79 % were obtained when 30 mg/L MW was used. Species including Acidithiobacillus ferrooxidans, Acidibacillus ferrooxidans and Leptospirillum ferriphilum were found predominant, accounting for more than 97 % according to 16 S rDNA analysis. Possible mechanism suggesting I- contained in MW worked as reducing agent to decrease Fe3+ hydrolysis and thus improving bioleaching was proposed.

Water physicochemical quality as driver of spatial and temporal patterns of microbial community composition in lake ecosystems

This study aimed at monitoring and management of the surface water and potentially pathogenic microbes of Lake Tonga (Algeria) with respect to. It characterized the main bacterial diversity patterns of Lake Tonga and predicted from water physicochemical parameters and water quality index (WQI) the distribution of bacterial species and the main indicator groups of faecal water contamination. Water samples were taken monthly at three sampling sites of different water depths. Several physicochemical parameters were measured; of which some were included in computing WQI to characterize the water quality of the lake. Counting, isolation and bacterial identification methods were used to characterize the existing aerobic heterotrophic bacteria. The composition of the microbial community of the waterbody of Lake Tonga included an abundant culturable bacterial flora belonging to several bacterial families and whose specific richness varied between water depths of the sites sampled. Species richness of the bacteria identified phenotypically varied between 7 and 11 per sample. The site with shallow water was the richest in bacterial species, compared to moderate and deep waters. The redundancy analysis showed the main physicochemical drivers of the microbial community composition. Our findings showed that high WQI scores indicated the water quality deterioration which triggered the increase in total load of faecal indicator bacterial groups. This study identified in Lake Tonga an important culturable aerobic bacterial flora whose specific richness and distribution varied spatially following the effects of water physicochemical parameters. Lake Tonga needs an integrated management plan to mitigate human disturbances declining water quality.

Hybrid sequence-based analysis reveals the distribution of bacterial species and genes in the oral microbiome at a high resolution

Bacteria in the oral microbiome are poorly identified owing to the lack of established culture methods for them. Thus, this study aimed to use culture-free analysis techniques, including bacterial single-cell genome sequencing, to identify bacterial species and investigate gene distribution in saliva. Saliva samples from the same individual were classified as inactivated or viable and then analyzed using 16S rRNA sequencing, metagenomic shotgun sequencing, and bacterial single-cell sequencing. The results of 16S rRNA sequencing revealed similar microbiota structures in both samples, with Streptococcus being the predominant genus. Metagenomic shotgun sequencing showed that approximately 80 % of the DNA in the samples was of non-bacterial origin, whereas single-cell sequencing showed an average contamination rate of 10.4 % per genome. Single-cell sequencing also yielded genome sequences for 43 out of 48 wells for the inactivated samples and 45 out of 48 wells for the viable samples. With respect to resistance genes, four out of 88 isolates carried cfxA, which encodes a β-lactamase, and four isolates carried erythromycin resistance genes. Tetracycline resistance genes were found in nine bacteria. Metagenomic shotgun sequencing provided complete sequences of cfxA, ermF, and ermX, whereas other resistance genes, such as tetQ and tetM, were detected as fragments. In addition, virulence factors from Streptococcus pneumoniae were the most common, with 13 genes detected. Our average nucleotide identity analysis also suggested five single-cell-isolated bacteria as potential novel species. These data would contribute to expanding the oral microbiome data resource.

A Comprehensive Study of Respiratory Pathogen Shifts in Response to the COVID-19 Pandemic: Insights from a Tertiary Level Hospital in Bangladesh

Introduction: Respiratory tract infections (RTIs) are a global health concern, with lower respiratory infections (LRIs) causing millions of deaths annually. The COVID-19 pandemic, caused by SARS-CoV-2, led to unprecedented public health measures, including lockdowns and vaccination campaigns, which have influenced the landscape of respiratory infections. This study aims to investigate the impact of COVID-19, its mitigation strategies and vaccination status on the prevalence and distribution of bacterial pathogens causing RTIs in a Bangladeshi hospital. Methods: Respiratory samples were collected from 100 patients with RTI symptoms in a teaching hospital in Bangladesh from December 2022 to May 2023. Bacterial cultures were performed, and antibiotic susceptibility testing was conducted. Patient data, including age, gender, comorbidities, and vaccination status, were analyzed statistically. Results: Among the participants, 96% exhibited bacterial growth in respiratory samples. Klebsiella pneumoniae was the most prevalent pathogen (63.2%), followed by Streptococcus spp. (12.2%) and Staphylococcus aureus (10.2%). The prevalence of these pathogens varied by age groups, with Klebsiella pneumoniae being prominent in the 50-69 age range. COVID-19 vaccination status significantly influenced the distribution of bacterial species, with fully vaccinated individuals having higher rates of certain infections, such as Klebsiella pneumoniae and Streptococcus spp. Comorbidities were also associated with variations in bacterial infections. Discussion: This study reveals a high prevalence of bacterial pathogens in post-COVID-19 RTIs, with Klebsiella pneumoniae being the predominant species. The findings suggest that COVID-19 vaccination status plays a crucial role in shaping the spectrum of bacterial infections, with fully vaccinated individuals showing a higher prevalence of specific pathogens. Comorbidities also influence the type and frequency of bacterial infections. These results align with previous studies and underscore the need for continued monitoring and research in the ever-evolving landscape of infectious diseases. Conclusion: The COVID-19 pandemic has brought significant changes to the patterns of respiratory infections. Understanding the impact of COVID-19 and vaccination status on respiratory pathogens is vital for healthcare providers and policymakers. This study emphasizes the importance of ongoing research and vigilance in addressing the evolving challenges of infectious diseases in the post-COVID-19 era. It highlights the interconnectedness of vaccination, immunity, and susceptibility to bacterial infections, providing critical insights for public health strategies.

Evaluation of prebiotic ability of xylo-oligosaccharide fractions with different polymerization degrees from bamboo shoot shells

The degree of polymerization of xylo-oligosaccharides (XOS) as prebiotics affects the gut microbiota’s metabolism. Herein, the differential prebiotic effects of original XOS solution and XOS solution enriched in X2-X3 (LDX) from bamboo shoot shells by hydrothermal pretreatment were investigated through intestinal microbiota in vitro. The findings demonstrated that the anaerobic cultivation of intestinal microbiota by XOS and LDX could increase its abundance by 1.8-fold and 2.3-fold with sugar utilization rates of 90% and 100%, respectively. The concentrations of produced short-chain fatty acids were 3.7 g/L and 6.4 g/L, respectively. The α-diversity analysis of gut microbiota revealed that the LDX group exhibited a lower species richness in microbial growth and a more evenness distribution of bacterial species compared to XOS group. The analysis of gut microbiota species composition highlights that LDX induced a more prominent proliferation of the Firmicutes phyla, while also displaying stronger inhibitory effects on the Proteobacteria phylum. Additionally, functional predictions suggested significant differences between XOS and LDX in terms of modulating the metabolism of gut microbiota, whereas LDX demonstrates its strength in inhibiting pathogenic bacterial communities. This research is to offer a theoretical foundation for the prebiotics made from bamboo shoot shells.

Gender Differences on Prevalence of Uropathogens and Their Antimicrobial Resistance: Results from a Single-Center Study in Peja Region, Kosovo

Background: Urinary tract infection (UTI) is the world’s second most common bacterial infection, behind respiratory tract infections, affecting people of all ages worldwide. It is the most common bacterial infection among females. The present study aimed to determine the local bacterial species distribution of UTI isolates between males and females in the Peja region. Methods and Results: This cohort longitudinal, prospective-retrospective study was conducted in the microbiological laboratories of Peja region, Kosovo. The research includes all urine samples tested for gram-negative bacteria during three years, 2018-2020. The comparison of male and female samples in terms of the type of bacteria isolated showed that the urinary infection in female patients was caused by E. coli, significantly more often than in male patients (86.31% vs. 62.87%, P=0.0000), while in the samples from male patients, Klebsiella spp. (12.05% vs. 3.68%, P=0.0000), P. aeruginosa (7.49% vs. 1.59%, P=0.0000), and Acinetobacter spp. (7.82% vs. 1.59%, P=0.0000), were detected significantly more often than female isolates. The prevalence of Proteus spp. was similar in male and female isolates (6.19% vs. 5.03%, P=0.3926). The results of the statistical analysis showed a statistically significant difference in the resistance of E. coli to the analyzed antibiotics depending on the gender of the patients. E. coli showed significantly higher resistance in male patients than in female patients to 12 of the 13 antibiotics that were used: ampicillin, amikacin, gentamicin, cefalexin, cefuroxime, cefotaxime, ceftazidime, ofloxacin, imipenem, piperacillin, nitrofurantoin, and trimethoprim/sulfamethoxazole. In both genders, E. coli showed the lowest resistance to imipenem and the highest resistance to ampicillin. Conclusion: Not only does the prevalence of uropathogens gram-negative bacteria differ by gender (greater frequency among women) but their antibiotic resistance also differs by gender (higher resistance among male patients).

Pre-Pandemic Distribution of Bacterial Species in Nasopharyngeal Swab Specimens from Pediatric and Adult Patients Detected via RT-PCR Using the Allplex Respiratory Panel.

Background: Recently, panel-based molecular diagnostics for the simultaneous detection of respiratory viruses and bacteria in nasopharyngeal swab (NPS) specimens have been highlighted. We identified the distribution of bacterial species in NPS specimens collected from pediatric and adult patients by employing RT-PCR (Allplex respiratory panel 4, RP4, Seegene) to estimate its applicability in a panel-based assay for detecting respiratory viruses. Methods: We used 271 and 173 NPS specimens from pediatric and adult patients, respectively. The results of the Allplex RP4 panel using NPS (NPS-RP4) from adult patients were compared with those of the Seeplex PneumoBacter ACE Detection assay (Seegene), which used sputum for testing (sputum-Seeplex). Results: A total of 147 specimens (54.2%) were positive for the NPS-RP4 panel in pediatric patients. There were 94, 77, 10, 3, 3, and 2 specimens that were positive for Haemophilus influenzae (HI), Streptococcus pneumoniae (SP), Mycoplasma pneumoniae (MP), Chlamydia pneumoniae (CP), Bordetella pertussis (BP), and B. parapertussis (BPP), respectively. Among 173 adult patients, 39 specimens (22.5%) were positive in the NPS-RP4. Thirty specimens were positive for HI, and 13 were positive for SP. One specimen tested positive for both MP and Legionella pneumophila (LP). CP, BP, and BPP results were all negative. However, 126 specimens (72.8%) had positive results with sputum-Seeplex (99 SP, 59 HI, three LP, and two MP), and the overall percentage of agreement between the two assays was 39.3% in the adult patients. Conclusions: Bacterial species in NPS from more than half of pediatric patients were detected. Performing the Allplex RP4 assay with NPS revealed additional respiratory bacteria that are not detected in current clinical practices, which do not include bacterial testing, demanding the use of sputum specimens. However, the use of NPS showed low agreement with standard assays using sputum in adult patients. Thus, more research is needed to develop a reliable RT-PCR method using NPS specimens in adult patients.

Distribution of Bacterial Species and Resistance Patterns in Surgical Site Infection after Prior Administration of Vancomycin and Tobramycin Intrawound Powdered Antibiotic Prophylaxis.

Evaluate the species distribution and resistance patterns of bacterial pathogens causing surgical site infection (SSI) after operative fracture repair, with and without the use of intrawound powdered antibiotic (IPA) prophylaxis during the index surgery. Retrospective cohort study. Academic, level 1 trauma center, 2018-2020. Fifty-nine deep SSIs were identified in a sample of 734 patients with 846 fractures (IPA [n = 320], control [n = 526]; open [n = 157], closed fractures [n = 689]) who underwent orthopaedic fracture care. Among SSIs, 28 (48%) patients received IPA prophylaxis and 25 (42%) of the fractures were open. Intrawound powdered vancomycin and tobramycin. Distribution of bacterial species and resistance patterns causing deep surgical site infections requiring operative debridement. Zero patients developed infections caused by resistant strains of streptococci, enterococci, gram-negative enterics, Pseudomonas , or Cutibacterium species. The only resistant strains isolated were methicillin resistance (19%) and oxacillin-resistant coagulase-negative staphylococci (16%). There was no associated statistical difference in the proportion of bacterial species isolated, their resistance profiles, or rate of polymicrobial infections between the IPA and control group. Most (93%) cases using IPAs included vancomycin and tobramycin powders. There were 59 SSIs; 28 (9%) in the IPA cohort and 31 (6%) in the control cohort ( P = 0.13). The use of local antibiotic prophylaxis resulted in no measurable increase in the proportion of infections caused by resistant bacterial pathogens after operative treatment of fractures. However, the small sample size and limited time frame of these preliminary data require continued investigation into their role as an adjunct to SSI prophylaxis. Therapeutic Level III. See Instructions for Authors for a complete description of levels of evidence.

Sterile body fluids infections: Profile of bacteria and their antimicrobial resistance pattern in a tertiary care hospital from Uttar Pradesh

Objectives: Infections of sterile body fluids are important and significant causes of mortality and morbidity, especially healthcare-associated infections. Species-level identification and antimicrobial resistance profile of bacteria are important determinants while selecting appropriate antimicrobials for empirical and targeted therapy. We conducted this study to observe the distribution of various bacteria and their antimicrobial resistance profile isolated from sterile body fluids. Materials and Methods: We conducted this study in a tertiary care teaching hospital from western Uttar Pradesh for a period of 2 years. All sterile body fluid samples were processed by conventional aerobic bacterial culture followed by their identification up to species level by conventional biochemicals following standard microbiological procedures. The antimicrobial susceptibility of the bacterial pathogens grown in culture was tested by Kirby–Bauer disk diffusion method and interpretation of susceptibility testing was done according to CLSI guidelines 2020. Results: A total of 1980 sterile body fluid samples were collected during the study period and 192 samples were found positive on culture for bacterial pathogens. Gram-negative bacilli (GNB) were predominantly isolated, comprising 83.33% in comparison to 16.67 % of Gram-positive cocci. Among Staphylococcus aureus isolates, 75% were methicillin-resistant S. aureus. All S. aureus isolates were sensitive against vancomycin and linezolid. Among GNB, 25% were extended-spectrum beta-lactamase producers while 62.5% were carbapenemase producers. All GNBs were sensitive to colistin. Conclusion: From this study, we concluded that the pathogenic bacteria implicated in infections of sterile body fluids are predominantly multidrug-resistant. There is a huge variation in data on the distribution of bacterial species isolated from sterile body fluids and their antimicrobial resistance patterns from different geographical locations and healthcare settings. Thus, data from a particular healthcare setting are important for empirical treatment in that healthcare setting.

Bacterial species distribution on the genital skin of hospitalized patients with stroke manifesting incontinence-associated dermatitis: A cross-sectional study.

To compare the isolated and identified bacterial species colonizing on the genital skin between patients with and without incontinence-associated dermatitis. This cross-sectional study included 102 patients with stroke admitted to an acute hospital in Japan. Swabs were collected, and bacterial species found in swabs were isolated and identified using a selective agar medium and simple identification kits. In addition to demographic information, severity of incontinence-associated dermatitis and the total bacterial counts were measured. Incontinence-associated dermatitis was present in 53.9% of the participants. Staphylococcus aureus was found in 50% of the participants with incontinence-associated dermatitis and only 17.9% of those without incontinence-associated dermatitis (P = 0.0029). Bacterial species distribution by erythema and skin erosion, which denote severity of incontinence-associated dermatitis, was different, but not significant; additionally, the total number of bacterial colonies was equivalent. Bacterial species distribution differed between patients with and without incontinence-associated dermatitis, whereas the total number of bacterial colonies was equivalent. A high detection rate of S. aureus on genital skin sites potentially affects the presence of incontinence-associated dermatitis and its severity. Geriatr Gerontol Int 2023; 23: 537-542.

Bactericidal Activity of Silver Nanoparticles on Oral Biofilms Related to Patients with and without Periodontal Disease

Background and Objectives: Periodontal disease (PD) is a multifactorial oral disease regularly caused by bacterial biofilms. Silver nanoparticles (AgNP) have offered good antimicrobial activity; moreover, there is no available scientific information related to their antimicrobial effects in biofilms from patients with PD. This study reports the bactericidal activity of AgNP against oral biofilms related to PD. Materials and Methods: AgNP of two average particle sizes were prepared and characterized. Sixty biofilms were collected from patients with (30 subjects) and without PD (30 subjects). Minimal inhibitory concentrations of AgNP were calculated and the distribution of bacterial species was defined by polymerase chain reaction. Results: Well-dispersed sizes of AgNP were obtained (5.4 ± 1.3 and 17.5 ± 3.4 nm) with an adequate electrical stability (−38.2 ± 5.8 and −32.6 ± 5.4 mV, respectively). AgNP showed antimicrobial activities for all oral samples; however, the smaller AgNP had significantly the most increased bactericidal effects (71.7 ± 39.1 µg/mL). The most resistant bacteria were found in biofilms from PD subjects (p < 0.05). P. gingivalis, T. denticola, and T. forsythia were present in all PD biofilms (100%). Conclusions: The AgNP showed efficient bactericidal properties as an alternative therapy for the control or progression of PD.

The Microflora Structure in the Digestive Tract, Culture Water, and Feed of Hybrid Grouper (Epinephelus fuscoguttatus♀ × E. polyphekadion♂) Cultured in an Outdoor Pond Based on a High-Throughput Sequencing Technique

Nutrition, disease, and general wellbeing can be affected by the microbial communities associated with the digestive tracts of aquaculture species. Different sections of aquaculture species’ digestive tracts have distinctive surfaces and structures, which can change microbial communities. The present study examined the composition and distribution of bacterial species in the intestine of hybrid grouper (Epinephelus fuscoguttatus E. polyphekadion) and its aquaculture environment. Using high-throughput pyrosequencing, a 16S rRNA sequence analysis was performed on hybrid grouper foregut, midgut, and hindgut, as well as cultured water and feed. There were 610,452 sequences obtained from five components (foregut, midgut, hindgut, water, and feed). Among operational taxa (OTUs), 506 of them were detected in the foregut, 605 in the midgut, 510 in the hindgut, and 573 in aquaculture water and feed samples. A total of 113 were detected in 5 samples. A species annotation revealed that hybrid grouper intestinal tracts were dominated by Proteobacteria (67.3%–73.7%), Firmicutes (8.4%–14.0%), and Actinobacteria (6.9%–10.5%). In aquaculture culture water, Proteobacteria were predominant (36.3%), Actinobacteria (30.0%), and Planctomycetes (14.0%). Acinetobacter (1.4%–17.9%) and Photobacterium (32.0%–57.5%) dominated the intestine. Photobacterium (3.6%) and Mycobacterium (7.1%) dominated the water bacteria. The water and intestine contained five potentially pathogenic bacteria: Pseudomonas, Flavobacterium, Escherichia coli, Aeromonas bacteria, and Vibrio. The highest proportion of Vibrio was found in the water (1.7%), while Pseudomonas dominated the midgut (2.6%). Six potential probiotics were detected in the aquaculture water and intestine (Lactococcus, Streptococcus, Bdellovibrio, Lactobacillus, Bacillus, and Bacteroides). Aquaculture water and intestines contained Bacillus, Bacteroides, and Lactobacillus. According to the findings, the intestinal flora of hybrid grouper is closely correlated with its pond culture environment. Results from the study provide an experimental basis for the controlled breeding of hybrid groupers and the regulation of their microecological processes in the breeding environment deepen our understanding of the intestinal bacterial population of healthy hybrid groupers.

Simultaneous Chemical Mapping of Live Biofilm Microenvironmental pH and Hydrogen Peroxide in Real Time with a Triple Scanning Electrochemical Microscopy Tip.

Dental plaque biofilm is a complex ecosystem. The distribution of microbial species in the biofilm is heavily influenced by local chemical interactions that result from diverse metabolic activities and the nature of the released molecules. As a relevant example, H2O2-producing bacteria can antagonize disease-associated bacteria, leading to the maintenance of a healthy oral microbiome. Herein, we report the development of a triple-sensor (redox, pH, and H2O2) scanning electrochemical microscopy (SECM) tip capable of simultaneously mapping the pH and H2O2 concentration produced by a dental plaque-derived multispecies biofilm grown on hydroxyapatite. The pH sensor of the triple SECM tip showed a near Nernstian slope of -71.1 ± 2 mV/pH (N = 3), whereas the H2O2 sensor showed a slope of -0.052 ± 0.002 nA/μM H2O2 at pH 7.2 and a detection limit of 1.0 ± 0.2 μM (N = 7). There is no significant difference in the sensitivities of H2O2 sensors at pH 6.2, 7.2, and 8.2 at 95% CI (N = 7). The pH and H2O2 sensors demonstrated excellent reversibility with response times of 3 and 5 s, respectively, along with reliable stability over 4 h at 37 °C. The sensors did not show any cross talk between pH and H2O2 concentration ([H2O2]) measurements, highlighting the accuracy and versatility of the SECM tip. Simultaneous chemical imaging of pH and [H2O2] across the biofilm revealed a clustered distribution of local H2O2 concentrations, ranging from 0 to 17 μM. Conversely, the local pH remained constant at 7.2. The relation of local chemical profiles and the distribution of bacterial species within the oral microbiome was experimentally investigated in the context of bacterial H2O2 antagonism. The benefit of clustered H2O2 production was that the total area of H2O2 produced by smaller clusters was 67% more than that of a single cluster with the same starting number of bacteria. Thus, this triple SECM tip can potentially be used to study local molecular mechanisms that result in dysbiosis of the oral microbiome.

Long-term mowing and burning have more of an effect on soil fungal communities than on bacteria in a semiarid sandy land

Mowing and burning, two common human disturbance methods, have different impacts on the soil fungal and bacterial communities of sandy land ecosystems in semiarid areas. Thus, the effects of long-term mowing and burning on plant and soil microbial communities in the semiarid Horqin Sandy Land are unclear. In this study, the effects of soil microbial community structure from mowing and burning on plant and soil microbial communities over six years were assessed by high-throughput sequencing. First, we found that mowing and burning significantly reduced vegetation coverage (V) (p < 0.05), and burning significantly increased plant Shannon–Wiener diversity (H), Pielou evenness (E), and Simpson dominance (λ) indices (p < 0.05). Second, the two human disturbances markedly affected fungal diversity and abundance more than bacterial diversity and abundance. In fungi, burning significantly reduced beta diversity (p < 0.05) and the relative abundance of Basidiomycota (p < 0.05) but markedly increased the relative abundance of Ascomycota and Mortierellomycota. Third, redundancy analysis (RDA) showed that vegetation coverage was a significant factor in bacterial species distribution (p < 0.05). For fungi, the significant factors were species richness (S) and vegetation coverage (p < 0.01). Taken together, these data suggest that long-term mowing and burning have more of an effect on soil fungal communities than bacteria in a semiarid sandy land, improving our understanding of how terrestrial ecosystems respond to human disturbances and providing guidance for the management and restoration of sandy desertification.

Breed and ruminal fraction effects on bacterial and archaeal community composition in sheep

While the breed of cattle can impact on the composition and structure of microbial communities in the rumen, breed-specific effects on rumen microbial communities have rarely been examined in sheep. In addition, rumen microbial composition can differ between ruminal fractions, and be associated with ruminant feed efficiency and methane emissions. In this study, 16S rRNA amplicon sequencing was used to investigate the effects of breed and ruminal fraction on bacterial and archaeal communities in sheep. Solid, liquid and epithelial rumen samples were obtained from a total of 36 lambs, across 4 different sheep breeds (Cheviot (n = 10), Connemara (n = 6), Lanark (n = 10) and Perth (n = 10)), undergoing detailed measurements of feed efficiency, who were offered a nut based cereal diet ad-libitum supplemented with grass silage. Our results demonstrate that the feed conversion ratio (FCR) was lowest for the Cheviot (most efficient), and highest for the Connemara breed (least efficient). In the solid fraction, bacterial community richness was lowest in the Cheviot breed, while Sharpea azabuensis was most abundant in the Perth breed. Lanark, Cheviot and Perth breeds exhibited a significantly higher abundance of epithelial associated Succiniclasticum compared to the Connemara breed. When comparing ruminal fractions, Campylobacter, Family XIII, Mogibacterium, and Lachnospiraceae UCG-008 were most abundant in the epithelial fraction. Our findings indicate that breed can impact the abundance of specific bacterial taxa in sheep while having little effect on the overall composition of the microbial community. This finding has implications for genetic selection breeding programs aimed at improving feed conversion efficiency of sheep. Furthermore, the variations in the distribution of bacterial species identified between ruminal fractions, notably between solid and epithelial fractions, reveals a rumen fraction bias, which has implications for sheep rumen sampling techniques.

Integrative effects of microbial inoculation and amendments on improved crop safety in industrial soils co-contaminated with organic and inorganic pollutants

Soils co-contaminated by organic and inorganic pollutants usually pose major ecological risks to soil ecosystems including plants. Thus, effective strategies are needed to alleviate the phytotoxicity caused by such co-contamination. In this study, microbial agents (a mixture of Bacillus subtilis, Sphingobacterium multivorum, and a commercial microbial product named OBT) and soil amendments (β-cyclodextrin, rice husk, biochar, calcium magnesium phosphate fertilizer, and organic fertilizer) were evaluated to determine their applicability in alleviating toxicity to crops (maize and soybean) posed by polycyclic aromatic hydrocarbon (PAHs) and potentially toxic metals co-contaminated soils. The results showed that peroxidase, catalase, and superoxide dismutase activity levels in maize or soybean grown in severely or mildly contaminated soils were significantly enhanced by the integrative effects of amendments and microbial agents, compared with those in single plant treatments. The removal rates of Zn, Pb, and Cd in severely contaminated soils were 49 %, 47 %, and 51 % and 46 %, 45 %, and 48 %, for soybean and maize, respectively. The total contents of Cd, Pb, Zn, and PAHs in soil decreased by day 90. Soil organic matter content, levels of nutrient elements, and enzyme activity (catalase, urease, and dehydrogenase) increased after the amendments and application of microbial agents. Moreover, the amendments and microbial agents also increased the diversity and distribution of bacterial species in the soil. These results suggest that the amendments and microbial agents were beneficial for pollutant purification, improving the soil environment and enhancing both plant resistance to pollutants and immune systems of plants.

Next Generation Sequencing genomic analysis of bacteria from soils of the sites with naturally-occurring summer truffle (Tuber aestivum Vittad.)

The rhizosphere is the region of soil in which the highest densities of fungi and bacteria occur. In this study, an attempt was made to assess the distribution of bacterial species in soil where the summer truffle Tuber aestivum Vittad. bears fruit in selected stands in Poland. In order to determine the bacterial metagenome, the Next Generation Sequencing (NGS) method was applied. Differences occurred in the bacterial species composition at the cluster level between soils in which summer truffle fruiting was recorded and control soils. In particular, differences in the percentage of Firmicutes bacteria were noted with an average frequency of 3.9% in truffle soil compared to 96.1% in the control soil. It was estimated that two bacterial species, namely Lysobacter antibioticus and Ensifer adhaerens had a positive effect on the occurrence of T. aestivum. Our research increased the knowledge of particular groups of bacteria accompanying truffles and their potential impact on the formation of fruiting bodies in T. aestivum.

Combination of Oxalobacter Formigenes and Veillonella Parvula in Gastrointestinal Microbiota Related to Bile-Acid Metabolism as a Biomarker for Hypertensive Nephropathy.

The human microbiome is a mixed group of microorganisms, which individually consists of 10–100 trillion symbiotic microbial cells. The relationship between gastrointestinal microbiota and blood pressure has been verified and the intestinal microbiota of chronic kidney disease (CKD) patients in the distribution of bacterial species is different from the flora of people with no CKD. The purpose of this research is to study the different intestinal microbiota of hypertensive patients with and without nephropathy and to find possible biomarkers of hypertensive nephropathy (H-CKD). The subjects of this research were divided into three groups, healthy control group, hypertension group, and hypertensive nephropathy group. Sequencing, bioinformatics, and statistical analysis were performed on the 16S rRNA gene of the subjects' stool samples. This research study showed the differences of intestinal flora as biomarkers in hypertension patients with and without nephropathy; it investigated the relationship of the differences in the intestinal microbiota with bile-acid metabolism; it also explored bile-acid metabolism mechanism of intestinal microbiota differences in hypertension with or without nephropathy. In summary, the difference in the combination of O. formigenes and V. parvula in the gastrointestinal microbiota is related to bile-acid metabolism in hypertensive patients and can be one of the factors causing CKD. It is the first time to report such a biomarker or pathogenic factor of H-CKD in the world.

One Day in Denmark: Nationwide point-prevalence survey of human bacterial isolates and comparison of classical and whole-genome sequence-based species identification methods.

ObjectivesImplementing whole-genome sequencing (WGS) technologies in clinical microbiology laboratories can increase the amount and quality of information available for healthcare practitioners. In this study, we analysed the applicability of this method and determined the distribution of bacterial species processed in clinical settings in Denmark.MethodsWe performed a point-prevalence study of all bacterial isolates (n = 2,009) processed and reported in the Clinical Microbiology Laboratories in Denmark in one day in January 2018. We compared species identification as performed by classical methods (MALDI-TOF) and by bioinformatics analysis (KmerFinder and rMLST) of WGS (Illumina NextSeq) data. We compared the national point-prevalence of bacterial isolates observed in clinical settings with the research attention given to those same genera in scientific literature.ResultsThe most prevalent bacterium was Escherichia coli isolated from urine (n = 646), followed by Staphylococcus spp. from skin or soft tissues (n = 197). The distribution of bacterial species throughout the country was not homogeneous. We observed concordance of species identification for all methods in 95.7% (n = 1,919) of isolates, furthermore obtaining concordance for 99.7% (n = 1,999) at genus level. The number of scientific publications in the country did not correlate with the number of bacterial isolates of each genera analysed in this study.ConclusionsWGS technologies have the potential to be applied in clinical settings for routine diagnostics purposes. This study also showed that bioinformatics databases should be continuously improved and results from local point-prevalence surveys should not be applied at national levels without previously determining possible regional variations.

Field-scale biostimulation shifts microbial community composition and improves soil pollution recovery at an artisanal crude oil refining site

ABSTRACT Hydrocarbon pollution has led to the destruction of farmlands and fishing settlements in the Niger Delta. In this study, DNA metabarcoding was used to investigate bacterial response during the remediation of an artisanal refining site. Total petroleum hydrocarbons reduced from 93,720 mg kg–1 on timepoint zero to 9,029.76 mg kg–1 on day 91. Bacterial species distribution significantly reduced during remediation. The most responsive phyla to the remediation approach were Proteobacteria and Cyanobacteria. Pathways for hydrocarbon degradation were differentially abundant during remediation. Overall, nutrient addition and intermittent tillage improved bacterial energy yield and the degradation of hydrocarbons.