Distinct soil bacterial patterns along narrow and broad elevational gradients in the grassland of Mt. Tianshan, China

Bacteria are essential regulators of soil biogeochemical cycles. While several studies of bacterial elevational patterns have been performed in recent years, the drivers of these patterns remain incompletely understood. To clarify bacterial distribution patterns and diversity across narrow- and broad-scale elevational gradients, we collected soil samples from 22 sites in the grasslands of Mt. Tianshan in China along three elevational transects and the overall elevation transect: (1) 6 sites at elevations of 1047–1587 m, (2) 8 sites at 876–3070 m, and (3) 8 sites at 1602–2110 m. The bacterial community diversity across the overall elevation transects exhibited a hump-like pattern, whereas consistent patterns were not observed in the separate elevational transects. The bacterial community composition at the phylum level differed across the transects and elevation sites. The Actinobacteria was the most abundant phylum overall (41.76%) but showed clear variations in the different transects. Furthermore, heatmap analyses revealed that both pH and mean annual temperature (MAT) were significantly (P < 0.05) correlated with bacterial community composition as well as the dominant bacterial phyla, classes, and genera. These findings provide an inclusive view of bacterial community structures in relation to the environmental factors of the different elevational patterns.

The Bacterial Pneumonia Characteristics based on Climate and Meteorological Parameters in Indonesia, the Tropical Country: A Preliminary Study

Introduction: As a tropical country, Indonesia has the potential to influence the characteristics of infectious diseases. The purpose of this study was to see how the pattern of pneumonia on various weather components such as rainfall, humidity, and temperature.Methods: This study was carried by retrospective screening in the infectious ward in one of the tertiary referral hospitals.Results: A total of 876 cases of pneumonia from eight treatment rooms were included in the study. The highest pneumonia cases occurred in February with 239 (27.2%) cases followed in April and May with 169 (19.2%) and 159 (18.2%) cases respectively. After microbiological examination, bacterial growth was found in 191 cases. The highest number of bacteria was found in February with 62 (32%), followed by May with 33 (17.2%) and April with 31 (16.2%) samples. Most of the bacterial grown were gram-negative (94.3%), dominated by Klebsiella pneumoniae (35%), followed by Acinetobacter baumanii 17.2% and Pseudomonas aeruginosa 12%. On the examination of antibiotic sensitivity, it was found that amikacin has a consistently high sensitivity (90%) for pneumonia caused by most bacterial causes (Acinetobacter baumanii, Klebsiella pneumoniae, and Escherichia coli).Conclusion: The study did not show any remarkable bacterial patterns based on weather components such as rainfall, humidity, and temperature during the rainy season. However, increasing the surveillance period will provide a better insight into the bacterial pattern and can compare it in the rainy and dry seasons.

In Vitro Selection of Probiotics, Prebiotics, and Antioxidants to Develop an Innovative Synbiotic (NatuREN G) and Testing Its Effect in Reducing Uremic Toxins in Fecal Batches from CKD Patients

We aimed to develop an innovative synbiotic formulation for use in reducing dysbiosis, uremic toxins (e.g., p-cresol and indoxyl sulfate), and, consequently, the pathognomonic features of patients with chronic kidney disease (CKD). Twenty-five probiotic strains, belonging to lactobacilli and Bifidobacterium, were tested for their ability to grow in co-culture with different vegetable (pomegranate, tomato, and grapes) sources of antioxidants and prebiotics (inulin, fructo-oligosaccharides, and β-glucans). Probiotics were selected based on the acidification rates and viable cell counts. Inulin and fructo-oligosaccharides reported the best prebiotic activity, while a pomegranate seed extract was initially chosen as antioxidant source. The investigation was also conducted in fecal batches from healthy and CKD subjects, on which metabolomic analyses (profiling volatile organic compounds and total free amino acids) were conducted. Two out of twenty-five probiotics were finally selected. After the stability tests, the selective innovative synbiotic formulation (named NatuREN G) comprised Bifidobacterium animalis BLC1, Lacticaseibacillus casei LC4P1, fructo-oligosaccharides, inulin, quercetin, resveratrol, and proanthocyanidins. Finally, NatuREN G was evaluated on fecal batches collected from CKD in which modified the viable cell densities of some cultivable bacterial patterns, increased the concentration of acetic acid and decane, while reduced the concentration of nonanoic acid, dimethyl trisulfide, and indoxyl sulfate.

Distinct soil bacterial patterns along narrow– and broad–scale elevational gradients in grassland of the Mt. Tianshan, China

Bacteria plays a crucial role in soil biogeochemical cycles, bacterial elevational patterns have been well studies over the past decade, but the elevational pattern and its driver poorly understood. To determine the distribution patterns of bacterial composition and diversity across narrow– and broad–scale elevational gradients, we collected soil samples from 22 sites in the grasslands of Mt. Tianshan along three elevational transects and the whole elevation transect: (1) 6 sites at 1047 m – 1587 m, (2) 8 sites at 876 m – 3070 m, and (3) 8 sites at 1602 m – 2110 m. We found a hump pattern of the bacterial community diversity on the whole elevation transect, while not have observed consistent patterns in separately elevation transect. Bacterial community composition based on phylum differed with transects and elevation sites. Furthermore, heatmap analysis showed that pH and MAT significantly (P < 0.05) correlated with bacterial community composition, dominant bacterial phylum and class significantly influenced soil pH. Therefore, our results suggested that soil property plays the most important role in shaping bacterial community patterns in grassland of Mt. Tianshan.

Characteristics and Patterns of Deep Neck Infection in Dr. Mohammad Hoesin General Hospital Palembang 2020

Intoduction: Deep neck infection is the accumulation of pus in the potential space and facial area in the deep neck. The incidence of deep neck space infections is 1/100.000 in adults and 2/100.000 in children. Risk factors such as age, oral hygiene, and comorbidities such as DM are predisposed factors in deep neck infection. Effective pus collection of specimens is essential, to obtain the organisms and determine the effective antibiotics. Purpose: The aim of this study was to describe the characteristics and bacterial patterns of abscess in Dr. Mohammad Hoesin General Hospital Palembang. Methods: This study was conducted retrospectively using medical records of patients who diagnosed deep neck infection in Dr. Mohammad Hoesin General Hospital Palembang during January to December 2020 who took pus collection and been checked in microbiology laboratory. Data recorded include gender, age, site, onset, risk factors, comorbidities, bacteria culture, antibiotic sensitivity, and complications. Results: Of the 36 patients, 23 (63.8%) were males, followed by 13 (36.1%) were female, and the age of 31-45 years old group were found in 13 subjects (36.1%). The onset was mostly found at 0-1 week as many as 19 subjects (52.7%). The highest complaints of dysphagia and odynophagia were found in 22 cases (26,2%), odontogenic factors were found in 35 cases (97,2%). Abscess location in multiple space were found in 17 cases (47,2%), while in single space there were 19 cases (52.7%), where the most location was in submandibular space in 7 cases. Diabetes was the most comorbid factors found in 6 subjects (50%). The most bacterial were Klebsiella pneumoniae in 4 cases (11.1%) and sensitive antibiotics including ciprofloxacin, meropenem, and tigecycline, in 6 cases (20%) respectively. And the most complication was mediastinitis in 6 cases (75%). Conclusion: Klebsiella pneumoniae is the most common found in deep neck infection with sensitive antibiotics including ciprofloxacin, meropenem, and tigecycline.

A performance comparison of the fully automated urine particle analyzer UF-5000 with UF-1000i and Gram staining in predicting bacterial growth patterns in women with uncomplicated urinary tract infections

Background The aim of this study was to compare the performance of the new flow cytometer UF-5000 with the UF-1000i and Gram staining for determining bacterial patterns in urine samples. Methods Women who attended our clinic with symptoms suggestive of urinary tract infection were enrolled in the study. Mid-stream urine samples were collected for gram staining, urine analysis and urine cultures. Bacterial patterns were classified using the UF-1000i (none, cocci bacteria or rods/mixed growth), the UF-5000 (none, cocci, rods or mixed growth) and Gram staining. Results Among the 102 included samples, there were 10 g-positive cocci, 2 g-positive bacilli, 66 g-negative rods, and 24 mixed growth. The sensitivity/specificity of the UF-1000i was 81.8/91.1% for gram-negative rods and 23.5/96.9% for cocci/mixed. The sensitivity/specificity of the UF-5000 was 80.0/88.2% for gram negative rods and 70.0/86.5% for gram-positive cocci. Conclusions The UF-5000 demonstrated good sensitivity and specificity for Gram-negative bacilli and demonstrated an improved sensitivity for detecting Gram-positive cocci compared with the UF-1000i.

Comparing the Performance of the New Fully Automated Urine Particle Analyzer UF-5000 with UF-1000i and Gram Stain in Predicting Bacteria Growth Patterns in Women with Uncomplicated Urinary Tract Infections

BackgroudTo compare the performance of the new flow cytometer UF-5000 with UF-1000i (Sysmex, Kobe, Japan) and Gram stain in predicting the bacterial patterns in urine samples MethodsWomen with symptoms suggestive of urinary tract infection were enrolled. Mid-stream urine sample was collected for gram staining, urine analysis and urine culture. Bacterial patterns were classified though UF1000i (none, cocci bacteria or rods/mixed growth), UF-5000 (none, cocci, rods or mixed growth) and Gram stain. Results Among the 102 samples, there were 10 gram-positive cocci, 2 gram-positive bacilli, 66 gram-negative rods, and 24 mixed growth. The sensitivity/specificity of the UF-1000i was 81.8/91.1% for gram-negative rods and 23.5/96.9% for cocci/mixed. The sensitivity/specificity of the UF-5000 was 80.0/88.2% for gram negative rods and 70.0/86.5% for gram-positive cocci.ConclusionsThe UF-5000 demonstrated the good sensitivity and specificity for Gram-negative bacilli bacteria and demonstrated an improved sensitivity for detecting Gram-positive cocci.

Intestinal microbiota as a key factor in the formation of immunity and tolerance. Probiotics capabilities

Introduction. The intestinal microbiome is an integral part of the health of its owner and performs several important functions: metabolic, coordinating, protective, epigenetic, which are closely interactive. In conditions of dysbiosis, disturbances of these functions contributes to different disorders.The intestinal immune system closely interacts with the microbiota. It is represented by all cells: T- and B-lymphocytes, T-regulatory, dendritic cells, macrophages. Micropresentation of antigens occurs through M-cells located between enterocytes. Toll-like receptors that recognize bacterial patterns are presented on the epithelial membrane. Dendritic cells present these antigens to T-cells and direct a further adaptive immune response.The immune system matures as a result of colonization of the intestine with microbiota, which is confirmed experimentally in gnotobiotic animals. Under physiological conditions, the immune system provides tolerance to its own microbiota through Tr-cells. Tolerogenic effects decrease in dysbiotic conditions, as a result, inflammation develops.The state of the intestinal barrier. The intestinal barrier is maintained by microbiota, which stimulates the synthesis of mucin and claudine. In dysbiosis, permeability increases, and the immune system is attacked by microbes and their metabolites, which contributes to inflammation.Dysbiosis predisposes to the development of inflammatory bowel diseases, colorectal cancer, metabolic syndrome and obesity, food allergies. In these diseases, the microbiota loses its diversity and richness and has a predominantly pro-inflammatory effect.The effect of probiotics on the immune system. Probiotics, due to adhesion to the mucous layer, enhance barrier functions, interact with the immune system, affect dendritic cells, promoting the formation of Tr and inhibiting the activation of NF-kB. Commensal metabolites (butyrate) increase the involvement of Tr cells in the colon, exerting a tolerogenic effect.Indications for the appointment of probiotics. Enterococcus faecium and Bifidobacterium longum have proven their activities similar to normal microbiota, and effectiveness in treatment of dysbiosis in children and adults.

Modelling collective cell motion: are on- and off-lattice models equivalent?

Biological processes, such as embryonic development, wound repair and cancer invasion, or bacterial swarming and fruiting body formation, involve collective motion of cells as a coordinated group. Collective cell motion of eukaryotic cells often includes interactions that result in polar alignment of cell velocities, while bacterial patterns typically show features of apolar velocity alignment. For analysing the population-scale effects of these different alignment mechanisms, various on- and off-lattice agent-based models have been introduced. However, discriminating model-specific artefacts from general features of collective cell motion is challenging. In this work, we focus on equivalence criteria at the population level to compare on- and off-lattice models. In particular, we define prototypic off- and on-lattice models of polar and apolar alignment, and show how to obtain an on-lattice from an off-lattice model of velocity alignment. By characterizing the behaviour and dynamical description of collective migration models at the macroscopic level, we suggest the type of phase transitions and possible patterns in the approximative macroscopic partial differential equation descriptions as informative equivalence criteria between on- and off-lattice models. This article is part of the theme issue ‘Multi-scale analysis and modelling of collective migration in biological systems’.