Bacterial Profiles Research Articles

The effect of coffee husks used as pellet bedding material on the intestinal barrier, immune-related gene expression and microbiota composition in the broiler chicken caecum

Abstract Introduction Using coffee husks as waste material for bedding contributes to sustainable development. A sustainable choice of bedding has also, however, to be a safe choice for poultry. The study analysed immune-related gene expression in the intestinal mucosa and indicator bacteria in caecal content collected from broiler chickens bedded on material with coffee husk addition. Material and Methods One-day-old Ross 308 chickens were divided into four groups of 10 birds each in five replicates: C, the control group kept on wheat straw bedding; CH10, a group kept on bedding of 10% coffee husks and 90% wheat straw; CH25, a group kept on bedding of 25% husks and 75% straw; and CH50, a group kept on bedding of 50% husks and 50% straw. After 42 days, the birds were slaughtered, the caecal mucosae were removed for RNA isolation and the caecal content was collected for bacterial DNA isolation. The expression of genes involved in intestinal immune response and host organism defence and the relative abundance of indicator bacteria were analysed. Results Upregulation of the expression of genes related to the immune response and intestinal tightness was correlated with an increase in the percentage of coffee husks in the pellet. Coffee husk pellets at 50% bedding content caused a significant numerical increase in Bifidobacterium and a statistically significant increase in Lactobacillus. A significant reduction in E. coli bacteria was also demonstrated in this group. Coffee husk pellets at all content percentages resulted in a statistically significant diminution of the level of Streptococcus bacteria. Conclusion The addition of coffee husks to poultry litter effects beneficial changes in the expression of genes related to intestinal health and the caecal bacterial profile.

Assessing Diagnostic Performance of Molecular Culture for Neonatal Sepsis: Protocol of the CHAMPIONS Study.

Managing neonatal sepsis is challenging due to nonspecific clinical signs, hematological markers with poor accuracy, and a lengthy turnaround time for the identification of microorganisms. Delaying the initiation of antibiotics in truly infected infants can lead to severe morbidity and mortality. Therefore, decisions regarding empiric antibiotic treatment are risk stratified, which exposes many uninfected infants to antibiotics. This causes gut microbiota perturbation, unnecessary hospital admissions, and the generation of multi-resistant organisms. High-speed diagnostic assays could expedite discontinuation or avert the initiation of antibiotics in uninfected infants. This study will evaluate the diagnostic performance of molecular culture (MC), a rapid broad-range PCR-based bacterial profiling technique, for diagnosing neonatal sepsis in infants below 90 days old. A multi-center prospective observational cohort study will include infants evaluated for early and late-onset sepsis. Routine evaluation for suspected sepsis includes microbiological cultures of blood. Additionally, blood for MC will be collected. For early-onset sepsis, umbilical cord blood may be used alternatively. Primary outcome is the agreement between MC and conventional blood culture results. Secondary outcome is the agreement of both assays with clinical sepsis using four different, commonly used definitions. Faster diagnostic pathways for sepsis may reduce antibiotic exposure time. Broad-range molecular assays may identify pathogens undetectable by conventional methods. Employment of umbilical cord blood samples for early-onset sepsis diagnosis can resolve challenges in collecting adequate blood volume and could further expedite treatment decisions.

Environmental Influence on Bacterial Lipid Composition: Insights from Pathogenic and Probiotic Strains.

The lipid composition of bacterial membranes is pivotal in regulating bacterial physiology, pathogenicity, and interactions with hosts. This study presents a comprehensive analysis of bacterial membrane lipid profiles across diverse Gram-positive and Gram-negative species. Utilizing matrix-assisted laser desorption/ionization (MALDI) in conjunction with advanced chemometric tools, we investigate the influence of environmental factors, isolation sources, and host metabolism on bacterial lipid profiles. Our findings unveil significant variations in lipid composition attributed to factors such as carbon/energy availability and exposure to chemicals, including antibiotics. Moreover, we identify distinct lipidomic signatures associated with pathogenic and probiotic bacterial strains, shedding light on their functional properties and metabolic pathways. Notably, bacterial strains isolated from clinical samples exhibit unique lipid profiles influenced by host metabolic dysregulation, particularly evident in conditions such as diabetic foot infections. These results deepen our understanding of the intricate mechanisms governing bacterial membrane lipid biology and hold promise for informing the development of innovative therapeutic and biotechnological strategies.

Bacterial community structure and metabolomic profiles of yak milk and cattle-yak milk during refrigeration in Gannan region: Analysis of interspecific differences in milk spoilage

The bacterial community dynamics and metabolomic profiles in raw yak (Y) milk and cattle-yak (CY) milk during refrigeration at 4 °C were investigated, followed by the elucidation of interspecific differences in milk storage. Bacterial communities and succession patterns were significantly different between the two milk types during refrigeration, with Lactococcus and Pseudomonas being the key distinguishing genera. Moreover, higher network complexity and tighter interactions were observed for the microbial community in CY milk than in Y milk. Furthermore, 7 proteases and 1 lipase potentially contributed to milk spoilage. The metabolomic profiles significantly differed between the milk types during refrigeration. Extended storage time decreased the relative abundances of organic nitrogen compounds and lipids and lipid-like molecules, with a concomitant increase in organic acids and derivatives, particularly in Y milk. Moreover, 9 metabolites, whose levels gradually increased with storage time, were strongly correlated with psychrophiles and thus considered potential markers of deterioration in plateau-characteristic milk. These findings offer a theoretical foundation for augmenting the quality and safety of plateau-characteristic milk and its derivatives, while also helping us understand the microbial and metabolic dynamics in raw milk under extreme environments.

Bacterial Profile and Antibiotic Susceptibility Patterns of Chronic Otitis Media at a Tertiary Care Center in Maharashtra.

Background Chronic otitis media (COM) is a persistent inflammatory condition of the middle ear and mastoid cavity, characterized by otorrhea and a perforated tympanic membrane. The microbial agents associated with COM vary over time and by geographic location. According to the WHO classification of countries based on COM prevalence, India is classified as having the highest prevalence (>4%) due to a national average of 7.8%, with the majority of the burden affecting individuals in lower socioeconomic strata. Objectives The objective of this study is to analyze the bacterial profile and antibiotic susceptibility patterns of isolates in patients with COM and to examine the age and gender distribution of these patients. Methods A cross-sectional microbiological study was conducted in the Department of Otorhinolaryngology at Dr. D. Y. Patil Medical College, Hospital & Research Centre, Dr. D. Y. Patil Vidyapeeth, Pune (Deemed to be University), Pune, India, from January 2023 to March 2023. The sample size was determined using WinPepi software. A total of 30 samples were collected from patients aged 5-15 years with active COM who presented to the ENT OPD. Patients who had been treated with antibiotics in the 15 days prior to the study were excluded. Results Of the 30 patients, most were in the age groups of 16-25 years (36.67%) and 26-35 years (16.67%), with only 10% in the 5-15 years age group. The age range of participants was eight to 55 years, with a mean age of 27 years. There was a gender disparity in the distribution of COM, with males representing 56.67% and females 43.33%, resulting in a male-to-female ratio of 1.3:1. The majority of patients had mucosal COM (24/30, 80%), while the remaining had squamosal COM (6/30, 20%). Pseudomonas aeruginosa was isolated in 24 samples (80%), and Staphylococcus aureus was identified in six samples (20%). Conclusion In the Indian context, where many predisposing factors for COM are prevalent, the disease remains highly common and can lead to severe complications if not treated promptly. This study analyzed ear swabs from 30 patients diagnosed with COM. The results revealed that P. aeruginosa was the most common microorganism, followed by S. aureus. The most effective antibiotics against P. aeruginosa were piperacillin-tazobactam, ceftazidime, and meropenem. For S. aureus, the most effective antibiotics included teicoplanin, vancomycin, linezolid, and cotrimoxazole.

Probiotic therapy modulates the brain-gut-liver microbiota axis in a mouse model of traumatic brain injury

The interplay between gut microbiota and host health is crucial for maintaining the overall health of the body and brain, and it is even more crucial how changes in the bacterial profile can influence the aftermath of traumatic brain injury (TBI). We studied the effects of probiotic treatment after TBI to identify potential changes in hepatic lipid species relevant to brain function. Bioinformatic analysis of the gut microbiota indicated a significant increase in the Firmicutes/Bacteroidetes ratio in the probiotic-treated TBI group compared to sham and untreated TBI groups. Although strong correlations between gut bacteria and hepatic lipids were found in sham mice, TBI disrupted these links, and probiotic treatment did not fully restore them. Probiotic treatment influenced systemic glucose metabolism, suggesting altered metabolic regulation. Behavioral tests confirmed memory improvement in probiotic-treated TBI mice. While TBI reduced hippocampal mRNA expression of CaMKII and CREB, probiotics reversed these effects yet did not alter BDNF mRNA levels. Elevated pro-inflammatory markers TNF-α and IL1-β in TBI mice were not significantly affected by probiotic treatment, pointing to different mechanisms underlying the probiotic benefits. In summary, our study suggests that TBI induces dysbiosis, alters hepatic lipid profiles, and preemptive administration of Lactobacillus helveticus and Bifidobacterium longum probiotics can counter neuroplasticity deficits and memory impairment. Altogether, these findings highlight the potential of probiotics for attenuating TBI's detrimental cognitive and metabolic effects through gut microbiome modulation and hepatic lipidomic alteration, laying the groundwork for probiotics as a potential TBI therapy.

Interaction Between Endometriosis and Bacteria in Infertile Women at Arash Women's General Hospital in Tehran

Background: Endometriosis is a common disorder that affects 20 - 50% of infertile women. The disease correlates with the presence of lactobacilli and changes in the number of Gram-negative and Gram-positive bacteria. Objectives: This article aims to investigate the interaction between endometriosis and certain bacteria. Methods: One hundred women between 18 and 40 years of age referred to the IVF department of Arash Women's Hospital in Tehran were studied. Fifty of them were diagnosed with endometriosis, while the rest were referred for investigation or freezing of their gametes or embryos. Specimens were collected from endometrial tissue and the cervix using swabs. These specimens were used for cultures and real-time PCR to quantify Lactobacillus. Results: Seventeen different Gram-positive and Gram-negative bacteria, as well as three yeasts, were isolated from women with and without endometriosis. The highest prevalence was related to Enterococcus faecalis, followed by Escherichia coli, Klebsiella pneumoniae, Staphylococcus aureus, E. faecium, Proteus mirabilis, Edwardsiella tarda, and Citrobacter spp. In cases with endometriosis, the relationship between the increase of Enterococcus spp., members of the Enterobacteriaceae family, and the decrease of lactobacilli was significant (P < 0.05). Staphylococcus aureus was isolated from the cervix of three women with endometriosis. The bacterial profiles of the cervix and endometrium were very similar. Conclusions: Considering the decrease of lactobacilli and the increase of other bacteria in people with endometriosis, it is recommended to use Lactobacillus and other probiotics for the prevention and even treatment of this disease.

Patterns of fluoroquinolone utilization and resistance in a tertiary care hospital: a retrospective cross-sectional analysis study from a developing country

BackgroundFluoroquinolones are the most commonly prescribed antibiotics. Because of their known tendency to drive antimicrobial resistance, their prescribing patterns need to be more restricted. This study aimed to describe the clinical practice of fluoroquinolone prescription, dose adjustments for renal impairment patients and bacterial resistance profiles, eventually providing evidence-based recommendations to optimize antibiotic prescribing practices in the local population.MethodsThis retrospective, cross-sectional study was conducted at An-Najah National University Hospital in Palestine. The data were collected from admitted patients who were given ciprofloxacin or levofloxacin from July 2021 to June 2023. Data from 692 inpatients across various hospital departments were examined (409 for levofloxacin and 283 for ciprofloxacin). Statistical analysis was performed via IBM SPSS version 23.0 to summarize the demographic, clinical, and epidemiological data.ResultsThe sociodemographic profile revealed diverse age distributions, with 25.4% and 39% older than 50 years for ciprofloxacin and levofloxacin, respectively. Ciprofloxacin was predominantly used in the oncology department (28.2%), with surgical prophylaxis (22.6%) and febrile or afebrile neutropenia (21.1%) being the most common indications. Levofloxacin was predominantly used in the medical ward (45.7%), mainly for lower respiratory tract infection (58.8%) and prophylaxis for bone marrow transplantation (16.5%). Enterococcus and methicillin-resistant Staphylococcus aureus were the most commonly isolated pathogens, with 62.5% of the isolates demonstrating resistance to ciprofloxacin. Moreover, extended-spectrum beta-lactamase-producing Enterobacterales were the most common pathogen isolated, with 33.3% being resistant to levofloxacin. Statistical analysis revealed a significant association between the choice of antibiotic and the approach to therapy. Levofloxacin was significantly more likely than ciprofloxacin to be used as empiric therapy (p < 0.001), whereas ciprofloxacin was more likely to be used as targeted therapy (p < 0.001).ConclusionsThis study investigated prescribing practices and resistance to levofloxacin and ciprofloxacin in a large hospital in a developing country. According to the bacterial resistance profiles, we conclude that there is a need for hospital departments to exercise greater restraint on the use of these antibiotics. To this end, further studies addressing the clinical efficacy of fluoroquinolones against the current treatment guidelines to evaluate their appropriateness should be carried out.

Perinatal Exposure to Phenols and Poly- and Perfluoroalkyl Substances and Gut Microbiota in One-Year-Old Children.

The role of the gut microbiota in human health calls for a better understanding of its determinants. In particular, the possible effects of chemicals with widespread exposure other than pharmaceuticals are little known. Our aim was to characterize the sensitivity of the early-life gut microbiota to specific chemicals with possible antimicrobial action. Within the SEPAGES French couple-child cohort, we assessed 12 phenols in repeated urine samples from 356 pregnant women and their offspring and 19 poly- and perfluoroalkyl substances (PFASs) in serum from the pregnant women. We collected stool samples from the children at one year of age, in which the V3-V4 region of the 16S rRNA gene was sequenced, allowing for gut bacterial profiling. Associations of each chemical with α- and β-diversity indices of the gut microbiota and with the relative abundance of the most abundant taxa were assessed using single-pollutant and mixture (BKMR) models. Perinatal exposure to certain parabens was associated with gut microbiota α- and β-diversity and with Firmicutes and Proteobacteria. Suggestive associations of certain phenols with genera of the Lachnospiraceae and Enterobacteriaceae families were observed, but these were not maintained after correction for multiple testing. Parabens, which have known antimicrobial properties, might disrupt the child gut microbiota, but larger studies are required to confirm these findings.

Gut bacterial community profile of frugivorous bats from Cathedral Cave in Cavinti, Laguna, Philippines.

Here we report the 16S rRNA gene amplicon analysis of the gut microbiota of three frugivorous cave bat species from the Cathedral Cave in Cavinti, Laguna, Philippines. Among the bat species, the most abundant phyla are Proteobacteria and Firmicutes D.

Sensory Textile-Bacterial Hybrids: Textile-Bacteria Fusion to Impart Forest-Associated Scents

This research paper presents a study on the development of living textile-bacterial hybrids, focusing on the scent produced by Streptomyces violaceruber, a bacterial species, throughout its growth phase. The objective of this study was to observe scent profiles of S. violaceruber on different fibres: cotton, acrylic, linen, and merino wool; and analyse the potential impact of fibre properties on scent profile, intensity, and duration. In doing so, the research suggests potential opportunities to curate living scents through textiles and the generation of sensory textile-bacterial hybrids. Interdisciplinary methods were applied to compare changes in the present volatile compounds and identify fibres and fabrication processes most suitable for creating a living textile. The paper reports on the development of textile samples that are infused with S. violaceruber and observed for their subjective scent, as well as the volatile compounds, which were analysed via gas chromatography. The findings of this study confirmed the presence and development of bacterial scents on textiles during bacterial growth. The scents identified included earthy, soil-like, floral, jasmine, and fruity notes, offering potential for further exploration in fibre and yarn selection, as well as the structural design of the textile. This research contributes to the field of biotextiles by examining the influence of textile fibres and knitted textiles on bacterial volatile compounds. It establishes a platform for investigating how different fibres and structural factors influence the bacterial scent profile. It also provides valuable insights for the future development of living sensory textiles and their integration into various applications.

Different Prostatic Tissue Microbiomes between High- and Low-Grade Prostate Cancer Pathogenesis.

Numerous human pathologies, such as neoplasia, are related to particular bacteria and changes in microbiome constituents. To investigate the association between an imbalance of bacteria and prostate carcinoma, the microbiome and gene functionality from tissues of patients with high-grade prostate tumor (HGT) and low-grade prostate tumor (LGT) were compared utilizing next-generation sequencing (NGS) technology. The results showed abnormalities in the bacterial profiles between the HGT and LGT specimens, indicating alterations in the make-up of bacterial populations and gene functionalities. The HGT specimens showed higher frequencies of Cutibacterium, Pelomonas, and Corynebacterium genera than the LGT specimens. Cell proliferation and cytokine assays also showed a significant proliferation of prostate cancer cells and elevated cytokine levels in the cells treated with Cutibacterium, respectively, supporting earlier findings. In summary, the HGT and LGT specimens showed differences in bacterial populations, suggesting that different bacterial populations might characterize high-grade and low-grade prostate malignancies.

Understanding bacterial diversity, infection dynamics, prevention of antibiotic resistance: an integrated study in an Algerian hospital context.

Bacterial infections, particularly bacteremia, urinary tract infections (UTIs), and pus infections, remain among hospitals' most worrying medical problems. This study aimed to explore bacterial diversity, infection dynamics, and antibiotic resistance profiles of bacterial isolates. We analyzed data from 1750 outpatients and 920 inpatients, of whom 1.6% and 8.47% respectively had various bacterial infections. The analysis revealed that UTIs were the most prevalent at 41.01%, particularly affecting women. UTIs also showed a distinct distribution across admission departments, notably in emergency (23.07%) and pediatric (14.10%) units. The most frequently isolated microorganisms were Escherichia coli (E. coli), followed by Klebsiella ornithinolytica. Skin infections followed UTIs, accounting for 35.88% of cases, more prevalent in men, with Staphylococcus aureus (S. aureus) being the primary pathogen (57%). Gram-negative bacteria (GNB) like E. coli and Pseudomonas aeruginosa contributed significantly to skin infections (43%). Bacteremia cases constituted 11.52% of bacterial infections, predominantly affecting women (67%) and linked to GNB (78%). A comparative study of antibiotic susceptibility profiles revealed more pronounced resistance in GNB strains isolated from inpatients, particularly to antibiotics such as Amoxicillin/clavulanic acid, Tetracyclin, Gentamicin, Chloramphenicol, and Ampicillin. In contrast, strains from ambulatory patients showed greater resistance to Colistin. Gram-positive bacteria from hospitalized patients showed higher resistance to quinolones and cephalosporins, while ambulatory strains showed high resistance to aminoglycosides, macrolides, fluoroquinolones, and penicillin. Furthermore, these analyses identified the most effective antibiotics for the empirical treatment of both community-acquired and nosocomial infections. Ciprofloxacin, aztreonam, and amikacin exhibited low resistance rates among GNB, with gentamicin and chloramphenicol being particularly effective for community-acquired strains. For S. aureus, ciprofloxacin, rifampicin, and cefoxitin were especially effective, with vancomycin showing high efficacy against community-acquired isolates and fosfomycin and chloramphenicol being effective for hospital-acquired strains. These results are essential for guiding antibiotic therapy and improving clinical outcomes, thus contributing to precision medicine and antimicrobial stewardship efforts.

In vivo absorption and fecal excretion of polysaccharides from the fruits of Lycium barbarum L. in rats through fluorescence labeling

In the present study, the in vivo absorption and fecal excretion of a purified fraction of polysaccharides from the fruits of Lycium barbarum L. (LBPs-4) in rats were investigated by labelling LBPs-4 with fluorescein isothiocyanate (FITC). It was found that the fluorescent labeled LBPs-4 (LBPs-4-FITC) was not detected in the plasma within 24 h following the administration of a single dose of LBPs-4-FITC (100 mg/kg of body weight) to rats, indicating that LBPs-4 was hardly absorbed in its prototype form. Instead, a smaller fragment dissociated from LBPs-4-FITC was observed in feces and was accumulated in a time-dependent manner, suggesting that LBPs-4 was excreted into the feces with a form of degradation. Meanwhile, we observed that LBPs-4-FTIC could modulate the fecal bacterial community profile via increasing the relative abundances of Bacteroides ovatus and Alistipes and promote the production of acetic acid. Furthermore, the monoculture experiment confirmed that LBPs-4 could be metabolized into smaller fragment by B. ovatus, producing acetic acid. Collectively, our study provides information on the destiny of LBPs-4 after oral administration: non-absorbed but moved to the large intestine and catabolized by gut microbiota, especially B. ovatus.

Early-life gut bacterial community structure predicts disease risk and athletic performance in horses bred for racing

Gut bacterial communities have a profound influence on the health of humans and animals. Early-life gut microbial community structure influences the development of immunological competence and susceptibility to disease. For the Thoroughbred racehorse, the significance of early-life microbial colonisation events on subsequent health and athletic performance is unknown. Here we present data from a three-year cohort study of horses bred for racing designed to explore interactions between early-life gut bacterial community structure, health events in later life and athletic performance on the racetrack. Our data show that gut bacterial community structure in the first months of life predicts the risk of specific diseases and athletic performance up to three years old. Foals with lower faecal bacterial diversity at one month old had a significantly increased risk of respiratory disease in later life which was also associated with higher relative abundance of faecal Pseudomonadaceae. Surprisingly, athletic performance up to three years old, measured by three different metrics, was positively associated with higher faecal bacterial diversity at one month old and with the relative abundance of specific bacterial families. We also present data on the impact of antibiotic exposure of foals during the first month of life. This resulted in significantly lower faecal bacterial diversity at 28 days old, a significantly increased risk of respiratory disease in later life and a significant reduction in average prize money earnings, a proxy for athletic performance. Our study reveals associations between early-life bacterial community profiles and health events in later life and it provides evidence of the detrimental impact of antimicrobial treatment in the first month of life on health and performance outcomes in later life. For the first time, this study demonstrates a relationship between early-life gut bacterial communities and subsequent athletic performance that has implications for athletes of all species including humans.

Effects of bacteriocin-producing Lactiplantibacillus plantarum on bacterial community and fermentation profile of whole-plant corn silage and its in vitro ruminal fermentation, microbiota, and CH4 emissions

BackgroundSilage is widely used to formulate dairy cattle rations, and the utilization of antibiotics and methane emissions are 2 major problems for a sustainable and environmentally beneficial ruminant production systems. Bacteriocin has received considerable attention because of its potential as an alternative to antibiotics in animal husbandry. However, the impact of bacteriocin-producing lactic acid bacteria on the microbiological conversion process of whole-plant corn silage and rumen fermentation remains limited. The purpose of this study was to assess the effect of 2 class IIa bacteriocin-producing strains Lactiplantibacillus plantarum ATCC14917 and CICC24194 on bacterial community composition and ensiling profiles of whole-plant corn silage and its in vitro rumen fermentation, microbiota, and CH4 emissions.ResultsBoth bacteriocin-producing strains increased the lactic acid concentration in silage fermented for 7 d, whereas the lowest lactic acid was observed in the ATCC14917 inoculated silage fermented for 90 d (P < 0.05). The highest DM content was observed in the CICC24194 treatment (P < 0.05), and the silages treated with both strains had the lowest DM loss (P < 0.05). Bacteriocin-producing strains promoted the growth of Levilactobacillus brevis on d 60 of ensiling. In addition, treatment with bacteriocin-producing strains increased the in vitro DM digestibility (P < 0.05) and decreased the CH4 production (P < 0.05). The results of random forest and clustering analyses at the genus level showed that ATCC14917 increased the relative abundance of the influential variable Bacillus compared to that in the control group, whereas CICC24194 decreased the relative abundance of the influential variable Ruminococcaceae UCG-005. The CICC24194 treatment had the lowest total bacterial, fungal, protozoan, and methanogen populations (P < 0.05).ConclusionsBoth class IIa bacteriocin-producing L. plantarum strains improved the fermentation quality of whole-plant corn silage by regulating the bacterial community composition during ensiling, with CICC24194 being the most effective. Both bacteriocin-producing strains mitigated CH4 production and improved digestibility by modulating the interactions among rumen bacteria, protozoa, methanogens, and the composition of fibrolytic bacteria.

Distinct drivers of bacterial community assembly processes in riverine islands in the middle and lower reaches of the Yangtze River.

Riverine islands are widespread alluvium wetlands developed in large rivers, and bacterial communities are crucial to their ecological function, yet their assembly processes are rarely addressed. The ecosystem services provided by the middle and the lower Yangtze are primarily threatened by pollution discharge from agricultural land use, and resource overutilization (e.g., embankments), respectively. Here, we assessed bacterial community assembly processes and their drivers within riverine islands in the middle Yangtze River (MR islands) and those in the lower reach (LR islands). A significant distance-decay relationship was observed, although the turnover rate was lower than that of the terrestrial ecosystem with less connectivity. Deterministic and stochastic processes jointly shaped community patterns, and the influence of stochastic increased from 26% in MR islands to 59% for those in LR islands. Meanwhile, the bacterial community in MR islands was controlled more by inorganic nitrogen availability, whereas those in LR islands were governed by pH and EC, although those factors explained a limited fraction of variation in the bacterial community. Potential indicator taxa (affiliated with Nocardioides and Lysobacter) characterized the waterway transport pollution. Overall, our study demonstrated that bacterial community dissimilarity and the importance of dispersal limitation increased concurrently along the flow direction, while distinct local factors further determined bacterial community compositions by selecting habitat-specificity taxa and particularly metabolism function. These findings enhanced our understanding of the mechanisms driving changes in bacterial communities of riverine islands subject to increased anthropogenic impacts.IMPORTANCERivers are among the most threatened ecosystems globally and face multiple stressors related to human activity. However, linkages between microbial diversity patterns and assembly processes in rivers remain unclear, especially in riverine islands developed in large rivers. Our findings reveal that distinct factors result in divergent bacterial community compositions and functional profiles in the riverine islands in the middle Yangtze and those in the lower Yangtze, with substantial differentiation in deterministic and stochastic processes that jointly contribute to bacterial community assemblages. Additionally, keystone species may play important metabolic roles in coping with human-related disturbances. This study provides an improved understanding of relationships between microbial diversity patterns and ecosystem functions under environmental changes in large river ecosystems.

Microbiological Landscape of Intensive Care Unit: A Retrospective Analysis of Bacterial Pathogens and Their Implications

Introduction: The intensive care unit (ICU) is a high-risk environment for hospital-acquired infections (HAIs) due to the complex interplay of patient vulnerability, invasive procedures, and the selective pressure of antimicrobial use. Understanding the local epidemiology of bacterial pathogens is crucial for effective infection prevention and control strategies. This study aimed to characterize the bacterial profile in an ICU setting, providing insights into the prevalent pathogens and their potential implications for patient care. Methods: A retrospective cross-sectional study was conducted, encompassing patients admitted to the ICU of Bangli Hospital Bali in 2023 and 2024. Data on patient demographics, sample sources, and microbiological findings were collected from medical records. Samples included blood cultures, sputum cultures (from both endotracheal tubes and spontaneous expectoration), wound swabs, and other sterile site cultures. Microbiological identification was performed using standard laboratory techniques. Results: A total of 219 patients were included in the study. The most common sample source was blood culture (42.9%), followed by sputum culture from endotracheal tubes (39.3%). A significant proportion of cultures showed no growth (34.7%), highlighting the challenges in identifying causative pathogens in the ICU. Among the identified pathogens, Staphylococcus spp. was predominant (15.5%), followed by Stenotrophomonas maltophilia (9.6%) and coagulase-negative staphylococci (8.7%). The distribution of pathogens varied across sample sources, with Staphylococcus spp. being prevalent in sputum cultures from endotracheal tubes and Klebsiella pneumoniae in sputum cultures. Conclusion: This study underscores the dynamic nature of the microbiological landscape in the ICU. The predominance of Staphylococcus spp., Stenotrophomonas maltophilia, and other opportunistic pathogens emphasizes the need for robust infection prevention and control measures. Further research is warranted to explore the impact of these pathogens on patient outcomes and to optimize antimicrobial stewardship in this critical care setting.

The influence of biotic and abiotic factors on the bacterial microbiome of gentoo penguins (Pygoscelis papua) in their natural environment

The microbiome is a key factor in the health, well-being, and success of vertebrates, contributing to the adaptive capacity of the host. However, the impact of geographic and biotic factors that may affect the microbiome of wild birds in polar environments is not well defined. To address this, we determined the bacterial 16S rRNA gene sequence profiles in faecal samples from pygoscelid penguin populations in the Scotia Arc, focusing on gentoo penguins. This mesopredatory group breeds in defined colonies across a wide geographic range. Since diet could influence microbiome structure, we extracted dietary profiles from a eukaryotic 18S rRNA gene sequence profile. The bacterial microbiome profiles were considered in the context of a diverse set of environmental and ecological measures. Integrating wide geographic sampling with bacterial 16S and eukaryotic 18S rRNA gene sequencing of over 350 faecal samples identified associations between the microbiome profile and a suite of geographic and ecological factors. Microbiome profiles differed according to host species, colony identity, distance between colonies, and diet. Interestingly there was also a relationship between the proportion of host DNA (in relation to total 18S rRNA gene signal) and the microbiome, which may reflect gut passage time. Colony identity provided the strongest association with differences in microbiome profiles indicating that local factors play a key role in the microbiome structure of these polar seabirds. This may reflect the influence of local transfer of microbes either via faecal-oral routes, during chick feeding or other close contact events. Other factors including diet and host species also associate with variation in microbiome profile, and in at least some locations, the microbiome composition varies considerably between individuals. Given the variation in penguin microbiomes associated with diverse factors there is potential for disruption of microbiome associations at a local scale that could influence host health, productivity, and immunological competence. The microbiome represents a sensitive indicator of changing conditions, and the implications of any changes need to be considered in the wider context of environmental change and other stressors.

Exploring oral bacterial compositional network in two oral disease groups using a convergent approach of NGS-molecular diagnostics.

Since most of the commonly known oral diseases are explained in link with balance of microbial community, an accurate bacterial taxonomy profiling for determining bacterial compositional network is essential. However, compared to intestinal microbiome, research data pool related to oral microbiome is small, and general 16S rRNA screening method has a taxonomy misclassification issue in confirming complex bacterial composition at the species level. Present study aimed to explore bacterial compositional networks at the species level within saliva of 39 oral disease patients (Dental Caries group: n = 26 and Periodontitis group: n = 13) through comparison with public Korean-specific healthy oral microbiome data. Here, we applied comprehensive molecular diagnostics based on qRT-PCR and Sanger sequencing methods to complement the technical limitations of NGS-based 16S V3-V4 amplicon sequencing technology. As a result of microbiome profiling at the genus level, relative frequencies of many nitrate-reducing bacteria within each oral disease group were found to be significantly low compared to the healthy group. In addition, the molecular diagnostics-based bacterial identification method allowed the determination of the correct taxonomy of screened primary colonizers (Streptococcus and Actinomyces unclassification clusters) for each oral disease. Finally, as with the results of microbiome profiling at the genus level, many core-species classified within the saliva of each oral disease group were also related to nitrate-reduction, and it was estimated that various pathogens associated with each disease formed a bacterial network with the core-species. Our study introduced a novel approach that can compensate for the difficulty of identifying an accurate bacterial compositional network at the species level due to unclear taxonomy classification by using the convergent approach of NGS-molecular diagnostics. Ultimately, we suggest that our experimental approach and results could be potential reference materials for researchers who intend to prevent oral disease by determining the correlation between oral health and bacterial compositional network according to the changes in the relative frequency for nitrate-reducing species.