16S rRNA Research Articles

DNA-metabarcoding of cyanobacteria and microalgae in chernozem soils of temperate continental climate of the forest-steppe zone of Eurasia under different degrees of agrotechnology intensification.

Chernozem soil is a valuable resource and contains a great diversity of microorganisms that play a global role in the process of soil formation, the species diversity of which has changed over the last five years under the influence of different agrotechnologies. For the first time, under the conditions of the Central Chernozem region, grain and fallow crop rotation, studies using the DNA-metabarcoding method were carried out to study the taxonomic structure of bacteria, fungi, cyanobacteria, and microalgae communities in the arable horizon of typical medium loamy chernozem under winter wheat cultivation. A comparative analysis of the composition of the genotypes showed significant differences in the presented level of mineral nutrition of the soil NPK (60) and NPK (100) compared with the control variant. After processing the 16S and 18S rRNA datasets, a similar trend of decreasing numbers of pro- and eukaryotic species was found from 6296 (control without MF) to 5310 with NPK (60) and to 4643 with NPK (100), respectively. The Chao1 index indicated that the expected diversity within the prokaryotic group was higher in the control without MF at 211, but decreased to 182 and 193 with NPK (60) and NPK (100) fertilizers, respectively. Analysis of the eukaryotic group revealed a 2.6- and 2.9-fold decrease in diversity by class and genus, respectively, depending on the nutritional levels in agrotechnologies, owing to the use of MF. In the prokaryotic community, Alphaproteobacteria microorganisms predominated at an amount of 14.20-14.46%, with Cyanophyceae accounting for 5.2-9.9%. The diversity of eukaryotes was smaller than the number of classes of prokaryotes; the main dominant were Zygnematophyceae 19.5-41%, Chlorophyceae occupied 10.4-15.8%. On the other hand, the doses of fertilizers used contributed to the emergence of dominant species adapted to high doses of mineral nutrients for plants.

Vertical stratification of arctic microbial communities near potential hydrocarbon seepage off Cape Dyer, Nunavut

AbstractClimate change disproportionately affects the Arctic, where warming is up to four times greater than the global annual average experienced in southern regions. Baffin Bay in the Canadian Arctic Archipelago is an ecologically and biologically significant area that will likely experience an increase in marine vessel traffic as a result of consistent declines in annual sea ice coverage. Along the western coast of Baffin Bay is known to be a region of active, natural hydrocarbon seeps where elevated levels of methane have been detected in previous surveys. Petroleum hydrocarbons released from the seafloor can fuel microbial production and shape the baseline microbiome. Establishing a microbial baseline is highly valuable as it contributes to a fundamental understanding of the existing microbial diversity that may be impacted in the future by anthropogenic stressors. In this study, 16S and 18S rRNA gene amplicon sequencing surveys revealed that the vertical stratification of the water column is largely driven by differences in depth, temperature, salinity, and inorganic nutrient concentrations. Chemical analysis provides further support that active petrogenic methane seepage occurs around Cape Dyer but not in areas targeted in this study. Presence of n-alkanes and toluene in association with hydrocarbon-synthesizing phytoplankton suggests biogenic production of these compounds. These findings provide a baseline for future environmental monitoring assessments to evaluate how the prokaryotic and eukaryotic microbiome may be impacted by ongoing climate change and anthropogenic stressors in western Baffin Bay.

Thioclava arctica sp. nov. and Zhongshania arctica sp. nov., isolated from the surface sediment of the Arctic Ocean and reclassification of Marortus luteolus Yu et al. 2019 as a later heterotypic synonym of Zhongshania marina On et al. 2019.

Two Gram-stain-negative bacterial strains, 15-R06ZXC-3T and R06B22T, were isolated from the surface sediment of the Arctic Ocean. Phylogenetic analyses based on the 16S rRNA gene and genome sequences indicated that strain 15-R06ZXC-3T belongs to the genus Thioclava, while strain R06B22T belongs to the genus Zhongshania. Strain 15-R06ZXC-3T showed the closest relationship to Thioclava indica DT23-4T. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strain 15-R06ZXC-3T and all of the type strains of the genus Thioclava ranged from 20.8 to 30.4% and 79.1 to 85.7%, respectively. Strain R06B22T was most closely related to Zhongshania marina DSW25-10T. The dDDH and ANI values between strain R06B22T and all of the type strains of the genus Zhongshania ranged from 18.6 to 20.4% and 77.5 to 79.4%, respectively. These dDDH and ANI values were all below the standard cutoff criteria for the delineation of bacterial species, indicating that the two strains may represent novel species within their respective genera. Furthermore, their phenotypic and chemotaxonomic characteristics also differentiated them from closely related species. Based on the polyphasic analyses, strains 15-R06ZXC-3T and R06B22T separately represent novel species of the genera Thioclava and Zhongshania, for which the names Thioclava arctica sp. nov. (type strain 15-R06ZXC-3T = MCCC 1A07434T= KCTC 8342T) and Zhongshania arctica sp. nov. (type strain R06B22T = MCCC 1A08273T= KCTC 8343T) are proposed. Additionally, phylogenomic analyses showed that the strain Marortus luteolus ZX-21T was clustered with the strain Z. marina DSW25-10T and all other type strains of the genus Zhongshania. Furthermore, the ANI and dDDH values between strains ZX-21T and DSW25-10T were 97.6% and 78.8±2.5%, respectively, strongly indicating that they represented a single species. Therefore, it is proposed that M. luteolus Yu et al. 2019 be recognized as a later heterotypic synonym of Z. marina On et al. 2019.

Nitrate-dependent antimony oxidase in an uncultured Symbiobacteriaceae member.

Autotrophic antimony (Sb) oxidation coupled to nitrate reduction plays an important role in the transformation and detoxification of Sb. However, the specific oxidase involved in this process has yet to be identified. Herein, we enriched the microbiota capable of nitrate-dependent Sb(III) oxidation and identified a new Sb(III) oxidase in an uncultured member of Symbiobacteriaceae. Incubation experiments demonstrated that nitrate-dependent Sb(III) oxidation occurred in the microcosm supplemented with Sb(III) and nitrate. Both the 16S rRNA gene and metagenomic analyses indicated that a species within Symbiobacteriaceae played a crucial role in this process. Furthermore, carbon-13 isotope labelling with carbon dioxide-fixing Rhodopseudomonas palustris in combination with nanoscale secondary ion mass spectrometry revealed that a newly characterized oxidase from the dimethylsulfoxide reductase family, designated as NaoABC, was responsible for autotrophic Sb(III) oxidation coupled with nitrate reduction. The NaoABC complex functions in conjunction with the nitrate reductase NarGHI, forming a redox loop that transfers electrons from Sb(III) to nitrate, thereby generating the energy necessary for autotrophic growth. This research offers new insights into the understanding of how microbes link Sb and nitrogen biogeochemical cycles in the environment.

Key Chemical Soil Parameters for the Assembly of Rhizosphere Bacteria Associated with Avocado Cv Hass Grafted on Landrace Rootstocks

Avocado cultivation holds significant economic importance in many countries, ranking Colombia as the fifth largest global producer. Particularly, the Hass cultivar plays a pivotal role in Colombia’s avocado industry, especially in the Department of Antioquia, the primary export region. This cultivar is grown under diverse soil and climate conditions and exhibits considerable genetic polymorphism due to the hybridization of varieties of agronomic significance, leading to a diverse array of landrace rootstocks. However, the role of soil conditions and rootstock genotype in structuring rhizosphere bacterial communities is still lacking. In addressing this knowledge gap, we investigated the influence of two soil conditions on the structure of rhizosphere bacterial communities associated with two landrace genotypes of Persea americana cv. Hass, utilizing 16S rRNA sequencing. Notably, no significant differences related to genotypes were observed. This study reports that the rhizosphere bacterial microbiome remains consistent across avocado landrace rootstocks, while variations in key parameters such as phosphorus, pH, Mg, and Ca drive distinct rhizosphere effects. Our results reveal that despite the soils having similar management, increases in these crucial parameters can lead to bacterial communities with lower alpha diversity and a more complex co-occurrence network. In addition, we found substantial variations in beta diversity, bacterial composition, and metagenome predictions between the two farms, underscoring the role of soil variables in shaping the bacterial microbiome. These findings provide valuable insights into the factors influencing the bacterial communities that may play a role in the health and productivity of crops with agro-industrial potential, such as Hass avocado.

Axis "microbiota – gut – eye": a review

Every organ in the human body has its own microbiota, and the eye, a complex multi-component organ, is no exception. Due to the limitations of traditional methods, detailed study of the ocular microbiome began only in 2010 as part of the Eye Microbiome Project, when advances in research methods made it possible to obtain detailed data, although there had been debate previously about whether microorganisms were even able to attach to the ocular surface due to the layers of the tear film, which have antibacterial properties. The cornea, conjunctiva, lacrimal glands and tear film, meibomian glands and microbiome form the microenvironment of the ocular surface, interacting together and resisting irritants, allergens and pathogens. Homeostasis of the ocular microbiota is critical for maintaining the health of the visual organ. Most microorganisms are found on the cornea and conjunctiva, and modern research methods, including 16S rRNA sequencing, have allowed us to establish the "core" of the ocular surface microbiota, identifying the most common types: Staphylococcus, Corynebacterium, Propionibacterium, and Streptococcus, although the exact composition of the “core” remains debatable. Many factors can influence the composition of the microbiome, including age, contact lens wear, ophthalmic medications, and antibiotics. Like the microbiome of many other organs, the ocular surface microbiome is influenced by the gut microbiome: this relationship has been called the "microbiota – gut – eye" axis. Within the "gut – eye" axis, healthy gut microbiota produce short-chain fatty acids, indoles, polyamines, and other substances that have a beneficial effect on the immune system and retinal health. The state of dysbiosis leads to disruption of homeostasis, and the increasing inflammatory reaction can contribute to damage to the optic nerve and progression of eye disease. Some ophthalmologic diseases, such as diabetic retinopathy, age-related macular degradation, choroidal neovascularization, uveitis, primary open-angle glaucoma, Sjogren's syndrome, dry eye syndrome are associated with dysbiosis of the intestinal microbial composition. Correction of intestinal dysbiosis using various methods can lead to a decrease in the risk of eye diseases, although additional research is needed to discover new methods for treating ophthalmologic pathologies along the "microbiota – gut – eye" axis.

Effect of probiotic supplementation combined with bismuth-containing quadruple therapy on gut microbiota during Helicobacter pylori eradication: a randomized, double-blind, placebo-controlled trial.

Helicobacter pylori (H. pylori) eradication has been reported to affect gut microbiota distribution. This study aimed to evaluate the effect of probiotic supplementation on the gastrointestinal microbiota during eradication and the efficacy of bismuth-containing quadruple therapy. One hundred treatment-naïve H. pylori-positive patients were randomly assigned 1:1 to receive 14-day bismuth-containing quadruple therapy (esomeprazole, bismuth, amoxicillin, and clarithromycin) combined with the probiotic (Bifidobacterium animalism subsp. lactis BLa80) or placebo. The Gastrointestinal Symptom Rating Scale (GSRS) was completed before and after treatment. Stool samples were collected for 16S rRNA gene sequencing at weeks 0, 2, and 10. No significant difference in the eradication rate was observed between the two groups. The incidence of adverse events, especially nausea (p = 0.029), was lower in the probiotic group. After treatment, the GSRS score decreased significantly in the probiotic group (p = 0.039). The gut microbiota underwent considerable changes immediately following eradication treatment, predominantly characterized by an increase in Proteobacteria at the expense of commensal Firmicutes and Bacteroidota, but gradually returned to baseline after eight weeks. By week 10, beneficial genera such as Lachnoclostridium, Parasutterella, Hungatella, and Akkermansia were notably enriched in the probiotic group. Additionally, the correlation networks in the probiotic group were closer to their initial levels at week 10 compared to the placebo group. Disturbances in the gut microbiota following H. pylori treatment appeared to be temporary, and probiotic supplementation could mitigate antibiotic-induced alterations in the gut microbiota. This study also provided evidence supporting the effectiveness of probiotics in alleviating gastrointestinal symptoms.

A pilot study examining periodontally healthy middle-aged humans and monkeys display different levels of alveolar bone resorption, gingival inflammatory infiltrate, and salivary microbiota profile.

Monkeys are an appropriate model for periodontal research owing to their similar dental anatomy and physiology unlike humans. Extensive literature exists on pathological periodontitis in monkeys and humans, although concerns regarding whether healthy middle-aged monkeys and humans display the same periodontal and oral microbial status remains unclear. The current study aimed to compare alveolar bone resorption, gingival inflammatory infiltrate, and salivary microbiota profile in periodontally healthy middle-aged humans and monkeys. CBCT examination and histological analysis were performed to compare the periodontal status in middle-aged healthy humans and monkeys. Oral saliva16S rRNA sequencing was performed to analyze the oral microbial profile. The alveolar resorption was compared between humans and monkeys, to determine the periodontal health. The percentage attachment of attachment loss was more around the posteriors teeth in humans when compared to monkeys (p<0.05). The degree of gingival inflammation was analyzed in both the groups, the expression of CD 34,45was higher in humans. 16S rRNA analysis demonstrated less diversity of salivary microorganisms in humans than in monkeys. The relative abundance of Aggregatibacter, Haemophilus, Gemella, and Porphyromonas at the genus level was significantly less in humans than in monkeys (p(<0.05). The periodontally healthy middle-aged humans and monkeys display different alveolar bone resorption and gingival inflammatory infiltrate levels. Furthermore, the salivary microbiota profile showed distinctly different oral microbiomes in these two primates. Our results suggest that the difference in alveolar bone status and gingival inflammatory infiltrate in healthy humans and monkeys might be associated with the diversity of the oral microbiome.

Altered Gut Microbiota Patterns in Young Children with Recent Maltreatment Exposure

Background: The brain and the intestinal microbiota are highly interconnected and especially vulnerable to disruptions in early life. Emerging evidence indicates that psychosocial adversity detrimentally impacts the intestinal microbiota, affecting both physical and mental health. This study aims to investigate the gut microbiome in young children in the immediate aftermath of maltreatment exposure. Methods: Maltreatment exposure was assessed in 88 children (ages 3–7) using the Maternal Interview for the Classification of Maltreatment [MICM]. Children were allocated to three groups according to the number of experienced maltreatment categories: no maltreatment, low maltreatment, and high maltreatment exposures. Stool samples were collected and analyzed by 16S rRNA sequencing. Results: Children subjected to high maltreatment exposure exhibited lower alpha diversity in comparison to those with both no and low maltreatment exposure (Simpson Index, Tukey post hoc, p = 0.059 and p = 0.007, respectively). No significant distinctions in beta diversity were identified. High maltreatment exposure was associated with the enrichment of several genera from the class Clostridia (Clostridium, Intestinibacter, Howardella and Butyrivibrio) and the depletion of the genus Phocaeicola (class Bacteriodia). Conclusions: Severe maltreatment exposure is associated with alterations in the gut microbiota of young children. Longitudinal trajectories of intestinal microbiota composition in the context of maltreatment may reveal important insights related to psychiatric and somatic health outcomes.

Beneficial effects of AMP Scy-hepc on the gut microbiota contribute to the potential growth of Larimichthys crocea

BackgroundIn light of the global ban on antibiotics in animal feed, antimicrobial peptides (AMPs) have emerged as a compelling substitute, garnering considerable interest for their potential as feed additives. Our previous study revealed that the extended (one-year) daily administration of the AMP Scy-hepc substantially boosted the growth of Larimichthys crocea. However, the exact influence of dietary supplementation with AMPs on the gut microbiota and the potential beneficial mechanisms remain unclear. Inspired by this, the present study endeavors to examine the alterations in gut microbiota at various gut sites in L. crocea following a 60-day Scy-hepc feeding regimen, building upon our prior research efforts.ResultsUtilizing 16S rRNA sequencing, we found that dietary supplementation with Scy-hepc significantly promoted the growth of L. crocea, which may be caused by the remarkable changes in the microbial communities within the foregut and midgut. Notable changes were observed in Tenericutes, Firmicutes, Proteobacteria, Cyanobacteria and Spirochaetes. The bacterial load trends in both the foregut and midgut demonstrated a notable increase following a 60-day Scy-hepc feeding, as determined by absolute quantitative PCR analysis. Moreover, Scy-hepc supplementation increased the abundance of potential probiotics (Rhodobiaceae and Planococcaceae) and reduced the abundance of opportunistic pathogens (Flavobacteriia and Mollicutes). This led to a more intricate microbial network with enhanced metabolism-related functions, especially in lipid transport and metabolism, signal transduction mechanisms, and coenzyme transport and metabolism. And the microbial resistance (Rs) exhibits no significant change between the Scy-hepc and control groups, indicating a minimal level of toxicity to the gut microbiota of L. crocea.ConclusionsIn summary, this study provides compelling evidences supporting the beneficial alteration of gut microbiota in the foregut and midgut as an underlying mechanism by which Scy-hepc feeding promotes host growth. These findings offer a novel perspective for investigating the advantageous effects of AMPs on fish health and the advancement of aquaculture.

Investigating the Potential of River Sediment Bacteria for Trichloroethylene Bioremediation

Trichloroethylene (TCE) is a prevalent groundwater contaminant detected worldwide, and microbes are sensitive indicators and initial responders to these chemical contaminants causing disturbances to their ecosystem. In this study, microbes isolated from San Marcos River sediment were screened for their TCE degradation potential. Among the twelve isolates (SAN1-12), five isolates demonstrated TCE degradation within 5 days at 25 °C and 40 mg/L of TCE concentration in the following order: SAN8 (87.56%), SAN1 (77.31%), SAN2 (76.58%), SAN3 (49.20%), and SAN7 (3.36%). On increasing the TCE concentration to 80 mg/L, the degradation efficiency of these isolates declined, although SAN8 remained the prominent TCE degrader with 75.67% degradation. The prominent TCE-degrading isolates were identified as Aeromonas sp. SAN1, Bacillus sp. SAN2, Gordonia sp. SAN3, and Bacillus proteolyticus SAN8 using 16S rRNA sequencing. The TCE degradation and cell biomass of Bacillus proteolyticus SAN8 were significantly improved when the incubation temperature was increased from 25 °C to 30 °C. However, both slightly acidic and alkaline pH levels, as well as higher TCE concentrations, lowered the efficacy of TCE degradation. Nevertheless, these conditions led to an increase in bacterial cell biomass.

Yoonia algicola sp. nov., Yoonia rhodophyticola sp. nov. and Yoonia phaeophyticola sp. nov., isolated from marine algae.

Three Gram-stain-negative, strictly aerobic, non-motile, oxidase- and catalase-positive, short-rod-shaped bacteria, designated as strains G8-12T, SS1-5T and BS5-3T, were isolated from marine algae in South Korea. Strain G8-12T exhibited optimal growth at 20-25 °C, pH 8.0 and 2.0-2.5% (w/v) NaCl, while strains SS1-5T and BS5-3T grew optimally at 25 °C, pH 7.0 and 1.5% NaCl. All strains contained ubiquinone-10 as the sole respiratory quinone, with phosphatidylglycerol and phosphatidylcholine as major polar lipids, and C18 : 1 ω7c and C16 : 0 as major fatty acids (>5 %); C18 : 1 ω7c 11-methyl and C18 : 1 2-OH were additionally identified as major fatty acids in strain SS1-5T. The genomic DNA G+C contents were 57.0, 58.3 and 56.4% for strains G8-12T, SS1-5T and BS5-3T, respectively. Strains G8-12T, SS1-5T and BS5-3T exhibited less than 74.8% average nucleotide identity (ANI) and 19.7% digital DNA-DNA hybridization (dDDH) values with each other, indicating that they represent different species. Phylogenetic analyses based on both 16S rRNA gene and genome sequences revealed that strains G8-12T, SS1-5T and BS5-3T form distinct phylogenetic lineages within the genus Yoonia. Relative to other closely related Yoonia species, these strains exhibited ANI and dDDH values below 83.5 and 26.9%, respectively, suggesting that they constitute novel species within the genus Yoonia. Based on their phenotypic, chemotaxonomic and phylogenetic characteristics, strains G8-12T, SS1-5T and BS5-3T represent three novel species of the genus Yoonia, for which the names Yoonia algicola sp. nov. (G8-12T=KACC 22753T=JCM 35790T), Yoonia rhodophyticola sp. nov. (SS1-5T=KACC 22649T=JCM 35753T) and Yoonia phaeophyticola sp. nov. (BS5-3T=KACC 22648T=JCM 35751T) are proposed, respectively.

Microbial exposure at birth and the development of behavioral temperament during the first three years of childhood.

We investigated cross-sectional and longitudinal associations between neonate microbial exposure and emerging behavioral temperament measures at the ages of 1, 2, and 3 years. Infants and mothers (n = 335) were extracted from the Kuopio Birth Cohort Study. Temperament was assessed using the Infant Behavioral and Early Childhood Behavioral Questionnaires. Microbial samples were collected from oral cavity at birth and the bacterial profiles were assessed using 16S rRNA gene sequencing. Microbial diversity was characterized using alpha and beta diversity metrics. Analyses were performed for the most abundant genera. The sample was analyzed as a whole, as well as divided into subgroups representing no antibiotic use during birth (n = 198) and those with antibiotic use during birth (n = 137). No significant associations were observed between microbial profiles and behavioral measures after Bonferroni corrections. Nevertheless, our pre-correction results indicated an association between increased behavioral temperament surgency in the first year and beta diversity (high abundance of Bacteroides, Faecalibacterium and Blautia, low abundance of Lactobacillus) in the antibiotic use group. Additionally, pre-corrections, a high relative abundance of Staphylococcus was associated with increased surgency through years 1, 2, and 3 in the no antibiotics group, prompting consideration into a possible link between antibiotic use and emerging behavioral temperament.

Department-specific patterns of bacterial communities and antibiotic resistance in hospital indoor environments

The hospital indoor environment has a crucial impact on the microbial exposures that humans encounter. Resistance to antibiotics is a mechanism used by bacteria to develop resilience in indoor environments, and the widespread use of antibiotics has led to changes in the ecological function of resistance genes and their acquisition by pathogens. By integrating the 16S rRNA Illumina sequencing and high-throughput-quantitative PCR approaches with water and air dust samples across seven departments in Peking University Shenzhen Hospital, China, this study yields intriguing findings regarding the department-specific variations, correlations and source tracing of bacteria, antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) within the hospital indoor environment. A notable observation was the pivotal role played by seasonal variations in shaping the bacterial composition across the entire hospital indoor environment. Another department-specific finding was the correlation between ARGs and MGEs abundance, which was evident in the overall hospital indoor environment, but not found in the blood test room, ophthalmology, and gynecology departments. Notably, as an important source of bacteria and ARGs/MGEs for the blood test room, the gynecology department also presented a close link between bacterial communities and the presence of ARGs/MGEs. Additionally, the results reiterate the importance of surveillance and monitoring of antibiotic resistance, specifically in Legionella spp. in man-made water systems, and highlight the significance of understanding genetic elements like Tp614 involved in gene transfer and recombination, and their impact on antimicrobial treatment efficacy. Key points•The department-specific variations, correlations and source tracing of bacteria, ARGs, and MGEs were uncovered in the hospital’s indoor environment.•Although each department exhibited consistent seasonal impacts on bacterial compositions, the co-occurrence between the presence of ARGs and MGEs was exclusively evident in the emergency, surgery, pneumology and otolaryngology departments.•The gynecology department emerged as a crucial source of bacteria, ARGs and MGEs within the hospital. Additionally, it was found to exhibit a significant correlation between bacterial communities and the presence of ARGs and MGEs.

Study on the Changes in the Microbial Community in Rhizosphere Soil of Blueberry Plants at Different Growth Stages

In order to clarify the relationship between mineral nutrients and rhizosphere microorganisms at different growth and development stages of blueberry (Vaccinium spp.), this work studied the dynamic changes in element content and microbial quantity in different parts of blueberry plants. The test material was a 12-year-old half-highbush blueberry variety (‘Beilu’). The changes in the mineral nutrient elements in leaves, branches and the soil of blueberry plants were studied at the full bloom stage (T1), green fruit stage (T2), mature stage (T3) and late mature stage (T4), and the correlations of the average contents of mineral elements in the four periods were studied. The bacterial community in the rhizosphere soil was determined and analyzed using 16S rRNA high-throughput sequencing technology. The results showed that the changes in other mineral elements in various parts of blueberry plants varied in different periods. Nitrogen (N) showed a downward trend in branches, leaves and soil, especially in leaves (p &lt; 0.05). The N contents in T2, T3 and T4 decreased by 9.9%, 26.4% and 29.9%, respectively. The N contents in the leaves and branches showed a downward trend at different growth stages, especially in leaves. The phosphorus (P) content in leaves showed a trend of increasing first and then decreasing, while it continued to increase in branches. The content of potassium (K) in leaves changed significantly, where it increased first and then decreased. The content of calcium (Ca) in leaves decreased first and then increased, while the content of magnesium (Mg) in branches and leaves decreased first and then increased, and the relative change was significant. The contents of iron (Fe) and zinc (Zn) in leaves decreased first and then increased, while the contents of manganese (Mn) and copper (Cu) were relatively stable. Cu decreased first and then increased in leaves and soil, and it increased first and then decreased in branches. The mineral nutrients in different growth stages of blueberry showed significant correlation in leaves, branches and soil. Mn in leaves was significantly positively correlated with P, Ca, Mg, Mn, Cu and Zn in soil (p &lt; 0.01). Nitrogen and calcium in leaves were significantly correlated with manganese and phosphorus in soil, respectively. Ca in branches was significantly positively correlated with N and K in soil and was significantly positively correlated with Zn in soil (p &lt; 0.01). Magnesium was significantly negatively correlated with iron in soil. The bacterial community structure of the blueberry rhizosphere soil changed significantly over time (p &lt; 0.05), and the relative abundance showed the following trend: T4 &gt; T2 &gt; T3 &gt; T1. At the phylum level, Proteobacteria, Acidobacteria, Actinobacteria, Chloroflexi and Verrucomicrobia were the dominant bacteria in different periods. Candidatus solibacter and Bryobacter were significantly higher in T1 and T3 than in T1 and T4. Bradyrhizobium flora increased significantly at T3. Sphingomonas increased significantly at T1 (p &lt; 0.05).

Evaluation of physico-chemical quality and occurrence of Salmonella in water from food retail outlets

Salmonella is one among the most important biological contaminants in drinking water that possess safety hazards to human life. Faecal contamination of the water, indirectly from the household sewage discharge, municipal sewage etc. attributes to the repeated detection of Salmonella in water. This study aimed to investigate the occurrence of Salmonella and physico- chemical quality evaluation of samples of water collected from food retail outlets of Thrissur and Kollam districts. A total of 50 water samples (25 each from Thrissur and Kollam districts) used for cooking purpose were collected over a period of six months, March to August 2023. Water samples were subjected to comparative evaluation of physico-chemical qualities viz., pH, turbidity, total dissolved solids (TDS) and hardness. Collected water samples were examined for Salmonella spp. by conventional culture method and PCR. Genus specific and virulence genes of the isolates were detected using polymerase chain reaction. The occurrence of Salmonella spp. in samples of water collected from Thrissur was 24 per cent whereas in Kollam district it was only four per cent. The overall occurrence of Salmonella spp. in samples of water collected from both districts was 14 per cent. Physico-chemical parameters of water samples viz., pH, turbidity, total dissolved solids and hardness were within the BIS prescribed standards. The molecular characterisation of Salmonella spp. detected 16S rRNA in all isolates but invA and spvA genes were detected only in 14.28 per cent of the isolates. Hence proper disinfection of water and food sanitation in the retail outlets will help to minimize the risk of foodborne pathogens Keywords: Salmonella, water, physico-chemical quality, food retail outlets

Full-length 16S rRNA gene amplicon analysis of gut microbiota in pigs fed with different diets in growing and finishing stages

The present study utilized full-length 16S rRNA gene sequencing to investigate the impact of dietary protein content on the composition and function of gut microbiota, and to analyze the gut microbiota of pigs in the growing (30 kg) and finishing (120 kg) stages under different feeding conditions. The results indicated that the gut microbiota was significantly different between pigs fed high- and low-protein diets. Comparing fecal samples from pigs at 30 and 120 kg, pigs at 30 kg showed a significant increase in the relative abundance of Clostridium butyricum, whereas at 120 kg, the abundance of Lactobacillus reuteri and Lactobacillus johnsonii decreased. To access the functional profiles and metabolic pathways based on amplicon sequence variants (ASVs), the microbiome of the 120 kg exhibited significant enrichments in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways related to metabolism-related category, including Alanine, aspartate and glutamate metabolism, Tyrosine and Thiamin metabolism, and Inositol phosphate metabolism. Meanwhile, analysis using the MetaCyc database showed that the metabolic pathways of the 30 kg group were significantly distinct when compared to the 120 kg of fecal samples. Overall, the findings indicated that the gut microbiota composition and function in the 30 and 120 kg fecal samples were markedly shaped by different dietary protein levels.

Paenibacillus suaedae sp. nov. and Paenibacillus violae sp. nov., isolated from the roots of Suaeda japonica Makino and Viola mandshurica W. Becker with plant growth-promoting potential.

Two novel Gram-positive strains, chi10T and PFR10T, were isolated from the roots of Suaeda japonica Makino and Viola mandshurica W. Becker, respectively. The strains are facultatively aerobic, rod-shaped, motile via peritrichous flagella and endospore-forming. Strains chi10T and PFR10T showed the highest 16S rRNA gene sequence similarity to Paenibacillus alvei DSM 29T (99.0%) and Paenibacillus planticolens LMG 31457T (99.3%). Furthermore, the phylogenetic and phylogenomic analyses demonstrated that strains chi10T and PFR10T were closely related to the genus Paenibacillus. The digital DNA-DNA hybridization (dDDH) values for strains used in the phylogenetic analysis and strain chi10T ranged from 19.6 to 28.4%, while for strain PFR10T, the values ranged from 19.8 to 53.5%, according to the Genome-to-Genome Distance Calculator 3.0, which were all less than 70%. Additionally, the dDDH value between strains chi10T and PFR10T was 22.0%, confirming that they are different species of the genus Paenibacillus. The average nucleotide identity between chi10T and PFR10T and other species of the genus Paenibacillus were 68.4-84.7% and 67.8-93.6%, respectively. In addition, the major polar lipids of chi10T and PFR10T consisted of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major fatty acid profile of strain chi10T was iso-C15 : 0 and anteiso-C15 : 0, whereas the major fatty acid profile of strain PFR10T was iso-C15 : 0, anteiso-C15 : 0 and iso-C16 : 0. The sole respiratory quinone in strains chi10T and PFR10T was menaquinone-7. Phylogenomic, phenotypic and genome analyses strongly indicated that chi10T and PFR10T could be two novel Paenibacillus species for which the names Paenibacillus suaedae sp. nov. (type strain chi10T = KACC 23258T = TBRC 17803T) and Paenibacillus violae sp. nov. (type strain PFR10T = KACC 23263T = TBRC 17804T) are proposed, respectively.

Effects of simulated low-temperature thermal remediation on the microbial community of a tropical creosote contaminated soil.

In the search for more sustainable remediation strategies for PAH-contaminated soils, an integrated application of thermal remediation and bioremediation (TEB) may allow the use of less impacting temperatures by associating heating to biological degradation. However, the influence of heating on soil microbiota remains poorly understood, especially in soils from tropical regions. This work investigated the effects of low-temperature heating on creosote-contaminated soil bacteria. We used culture-dependent and 16S rRNA sequencing methods to compare the microbial community of soil samples heated to 60 and 100 oC for 1h in microcosms. Heating to 60°C reduced the density of cultivable heterotrophic bacteria compared to control soil (p < 0.05), and exposure to 100°C inactivated the viable heterotrophic community. Burkholderia-Caballeronia-Paraburkholderia (BCP) group and Sphingobium were the predominant genera. Temperature and incubation time affected the Bray-Curtis dissimilarity index (p < 0.05). At 60°C and 30 days incubation, the relative abundance of Sphingobium decreased and BCP increased dominance. The network of heated soil after 30 days of incubation showed fewer nodes and edges but maintained its density and complexity. Both main genera are associated with PAH degradation, suggesting functional redundancy and a likely potential of soil microbiota to maintain biodegradation ability after exposure to higher temperatures. We concluded that TEB can be considered as a potential strategy to bioremediate creosote-contaminated soils, allowing biodegradation in temperature ranges where thermal remediation does not completely remove contaminants. However, we recommend further research to determine degradation rates with this technology.

Exploring the potential role of microbiota and metabolites in acute exacerbation of chronic obstructive pulmonary disease.

The acute exacerbation of chronic obstructive pulmonary disease seriously affects the respiratory system function and quality of life of patients. This study employed 16S rRNA sequencing and metabolomics techniques to analyze the respiratory microbiota and serum metabolites of COPD and AECOPD patients. The results showed that the microbial diversity in the respiratory tract of AECOPD patients was significantly lower than that of COPD patients, and the relative abundance of Bacteroidetes, Prevotella and Neisseria in the respiratory tract of AECOPD patients was significantly lower than that of COPD patients. However, the relative abundance of Haemophilus_D, Veillonella_A and Pseudomonas_E, in AECOPD patients was significantly higher than that of COPD patients, and the ability of respiratory microbiota in AECOPD patients to participate in alanine metabolism was significantly lower than that of COPD patients. Metabolome results further revealed that the serum alanine levels in AECOPD patients were significantly lower than those in COPD patients, and these differential metabolites were mainly involved in linoleic acid metabolism, protein digestion and absorption and regulation of lipolysis in adipocytes. In summary, the structural characteristics of respiratory microbiota in COPD and AECOPD patients are different from those in healthy populations, and their microbiota diversity decreases and microbial community structure and function will also undergo changes when acute exacerbations occur. In addition, the predicted microbial community function and metabolomics results indicate that the onset of AECOPD is mainly related to energy and amino acid metabolism disorders, especially alanine metabolism.