Analysis Of Microbial Populations Research Articles

PSLBI-20 Dynamic response of piglets fed different sources and levels of fiber during an enterotoxigenic Escherichia coli (ETEC) challenge in the post-weaning transition

Abstract Dietary fiber can stimulate the growth of volatile fatty acid-producing bacteria, hence promoting gut health. A stimbiotic can accelerate the settlement of a fiber-fermenting microbiome after weaning. The present study aimed to investigate how different fiber types and a stimbiotic can support microbiome function and resilience of piglets facing an F18 ETEC challenge. Newly weaned piglets (n = 216) were blocked by body weight (BW) and randomly assigned to 1 of 4 dietary treatments (n = 9), including a corn-soy and wheat middlings control diet (CTL), high fiber diet (HF), CTL plus 0.01% stimbiotic (CS; Signis; AB Vista, UK), and HF plus 0.01% stimbiotic (HFS). The HF diets included sugar beet pulp at 5.0%, 3.8%, 2.5% and soy hulls at 4.0%, 3.0% and 2.0% for phases 1 (d 0 to 9), 2 (d 0 to 16), and 3 (d 16 to 22), respectively. A standard diet was fed during phase 4 (d 22 to 41). On d 5 post-weaning, all pigs were orally inoculated with 10 mL of F18 ETEC (108 CFU/mL). Twelve piglets were selected from different pens, and a fecal sample was collected on d 5 before challenge (0 d post-inoculation; dpi), d 12 (dpi 7) and d 29 (dpi 24) for analysis of microbial populations by qPCR and fecal calprotectin. Statistical analyses consisted of a multivariate analysis by age, with fiber, stimbiotic, and their interaction as fixed effects. There was no main effect of fiber or stimbiotic on final BW, and d 0 to 40 average daily gain (ADG) or gain to feed (G:F; P > 0.10). Overall, pigs fed CS had a greater intake than HFS (P < 0.05) with CTL and HF intermediate. Piglets fed CS and HF tended to have greater ADG from d 0 to 22 compared with pigs fed CTL (P < 0.10). Piglets fed CS tended to have heavier d 22 BW than CTL (P < 0.10), with HF and HFS intermediate. On dpi 0, butyrate-producing bacteria Lachnospiraceae and Ruminococcaceae were increased in piglets fed a stimbiotic (P < 0.05). On dpi 0 and 7, piglets fed HF had increased abundance of Lachnospiraceae (P < 0.05), whereas no difference was observed on dpi 24 (P > 0.10). Total E. coli did not vary between groups (P > 0.10). On dpi 0, calprotectin concentration was similar between treatments (averaged 25 ng/g feces; P > 0.10) Calprotectin was less in piglets fed a stimbiotic, at 7 vs 22 ng/g feces on dpi 7, and 8 vs 19 ng/g feces on dpi 24 in the stimbiotic and no stimbiotic group, respectively (P < 0.05). There was no fiber or fiber × stimbiotic interaction for calprotectin (P > 0.10). These results demonstrate that feeding high fiber may accelerate the settlement of the piglet microbiome profile as early as 5 d post-weaning. Feeding a stimbiotic may support the resilience of piglets facing an F18 ETEC challenge by promoting the growth of butyrate-producing bacteria, which alleviates the gastrointestinal tract inflammation response and ultimately boost growth performance.

Organic acid preservation of cereal grains improves grain quality, growth performance, and intestinal health of post-weaned pigs

This study investigated the effect of preserving wheat and barley grains with an organic acid liquid surfactant mould inhibitor compared to conventional artificial drying and assessed its effects on the health and performance of pigs post-weaning (PW). A 2 × 2 factorial arrangement was conducted to investigate the interaction between grain preservation method (dried vs. preserved) and zinc oxide (ZnO) inclusion (yes vs. no) on growth performance, diarrhoea scores and incidence, and total tract nutrient digestibility. One hundred and ninety-two pigs (3 pigs/pen; 16 replicates/treatment) were assigned to one of four experimental diets for 35 days: (1) dried grain diet, (2) preserved grain diet, (3) dried grain diet with ZnO and (4) preserved grain diet with ZnO. Diets were formulated to contain similar levels of net energy and standardised ileal digestible lysine. On day 35 PW, 24 pigs (12 replicates/treatment) from the non-ZnO supplemented groups were euthanised and digesta was collected for coefficient of apparent ileal digestibility (CAID), gut microbial population and volatile fatty acid analysis. Stomach tissue was also collected for gene expression analysis, as well as small intestine samples for gut morphology. Notable improvements in grain quality were observed in the preserved grain, including a reduction in grain pH, mould presence, and contamination by mycotoxins, specifically deoxynivalenol in wheat and barley, and ochratoxin A and HT-2 toxin in barley. The preserved grain diet improved average daily gain (ADG; P < 0.01) and body weight (BW; P < 0.01) compared to the dried grain diet. The incorporation of ZnO increased average daily feed intake (ADFI; P < 0.01) and BW (P < 0.05) in the dried grain diet, however, ZnO did not affect ADFI (P > 0.05), and reduced ADG and BW in the preserved grain diet (P < 0.05). Pigs offered the preserved grain diet had reduced faecal scores and diarrhoea incidence compared to those offered the dried grain diet (P < 0.05). Supplementation of ZnO reduced faecal scores and diarrhoea incidence compared to non-supplemented pigs (P < 0.001). On day 35 PW, the preserved grain diet had improved CAID of nitrogen and gross energy (P < 0.05), lower levels of colonic branched-chain volatile fatty acids (P < 0.05), and beneficial shifts in gut microbial populations. Specifically, there was a reduction in ileal Streptococcus (P < 0.001) and an increased abundance of colonic Faecalibacterium (P < 0.05). In conclusion, organic acid preservation improved grain quality, benefiting post-weaned pigs through improved nutrient digestibility and gut health, thus enhancing overall growth performance PW.

Effects of different microbial agent applications on the growth and quality of saffron (Crocus sativus L.) cormels

Saffron (Crocus sativus L.) is a bulbous flower whose dried stigmas are used as a herbal medicine and as a spice. Saffron is cultivated worldwide, but corm degradation is an important factor affecting its yield and quantity. This study investigated the effects of three different microbial agents (Bacillus megaterium, Brevibacillus laterosporus, Paenibacillus mucilaginosus) on the growth and quality of saffron cormels. Both the weight and circumference of the cormels were significantly increased in response to microbial agent treatment. Measurements of the physiological and biochemical characteristics of the cormels as well as the flowering traits showed that the starch and protein contents as well as the flowering rate and stigma yield increased significantly after the application of the three microbial agents. Analyses of soil physicochemical properties and microbial populations revealed increases in the soil potassium content and a significant alteration in the soil microbial community structure in response to treatment. Our results showed that the application of three microbial agents enhances the growth, nutritional status and health of saffron cormels and improves the soil environment during saffron corm cultivation. Paenibacillus mucilaginosus also increased the accumulation of crocins and picrocrocin in stigmas. Our results provide the theoretical and practical knowledge needed to reduce corm degradation and to improve saffron corm cultivation.

Development and characterization of edible and active coating based on xanthan gum nanoemulsion incorporating betel leaf extract for fresh produce preservation

Developing an edible and active coating, incorporating environmentally-friendly antimicrobial agents into edible polymers, provides an eco-friendly alternative to conventional packaging and exhibits significant potential in preserving the quality of postharvest food. Herein, we aim to develop a novel edible and active coating based on xanthan gum (XG) nanoemulsion (NE) incorporating betel leaf extract (BLE) for the preservation of fresh produce. The total phenolic content, total flavonoid content, and antioxidant capacity of the methanol extract of BLE at various concentrations were characterized. Further development of the active coating at different formulations of Tween 80 (1 % and 3 % w/v), XG (0.1 % to 0.5 % w/v), and BLE (1 % to 5 % w/v) was characterized by physical stability, viscosity, and antimicrobial properties. Results showed that the active coating at 1 % BLE showed significant antimicrobial properties against diverse bacterial and fungal foodborne pathogens (e.g., B. cereus, S. aureus) and fungal cultures (e.g., C. albicans). The study also examined the shelf-life of tomatoes coated with the BLE-XG NE solution, stored at 4 °C for 27 days. Analyses of weight retention, soluble solids, pH, texture, sensory attributes, and microbial populations showed that the coating effectively preserved tomato quality, highlighting its potential to preserve fresh produce and enhance food security.

Unveiling the microbiota-metabolite-myocardium axis: a novel perspective on cardiovascular health.

Cardiovascular diseases, including myocardial infarction, remain a leading cause of death globally. Emerging evidence suggests the gut microbiota plays a crucial role in cardiovascular health. This study aims to explore the impact of gut microbiota on myocardial infarction using a mouse model. The research utilizes a multi-omics approach, including 16S rDNA sequencing and LC-MS-based metabolomics to analyze fecal and serum samples from mice modeled to mimic myocardial infarction. This methodology allows for a comprehensive analysis of microbial populations and their metabolic output. The findings reveal a significant reduction in gut microbiota α-diversity in mice with induced myocardial infarction compared to healthy controls. Notably, there is an increase in populations of Fusobacteria and Clostridia. Metabolomic analysis indicates disruptions in amino acid and energy metabolism, suggesting a metabolic dysregulation linked to myocardial health. The study proposes a novel microbiota-metabolite-myocardium axis, where specific microbial metabolites may directly affect heart health. This connection points to the gut microbiota as a potential player in the pathogenesis of myocardial infarction and may open new therapeutic avenues targeting the gut microbiome to combat cardiovascular diseases.

Performance of Fe-dosing membrane bioreactor and evaluation of phosphorus recovery as vivianite after long-term operation

In this study, the influence of high concentration of iron on the nutrient removal, membrane fouling and microbial diversity of membrane bioreactor for wastewater treatment were systematically investigated. Moreover, the potential of phosphorus recovery in the form of vivianite was assessed after the long-term operation. The results show that TP concentration in effluent was decreased to 1.07 ± 0.47 mg/L (without Fe addition), 0.41 ± 0.23 mg/L (Fe/P = 2), 0.20 ± 0.12 mg/L (Fe/P = 4). Compared with control group, the TN concentration in effluent was higher at the high concentration of iron, which was due to the decreased nitrite-oxidizing bacteria (NOB) by microbial population analysis. Membrane fouling was alleviated by enlarging floc size and reducing supernatant COD via adding iron. Besides, it was detected that the amorphous ferric oxide and Fe(III) bound phosphorus were the main Fe and P speciation and vivanite (ca. 29 %). The anaerobic environment was conducive to the formation of vivianite and the phosphorus recovery as vivanite was recommended based on the results of current study.

The distribution characteristics of aerosol bacteria in different types of sheepfolds.

With the development of modern sheep raising technology, the increasing density of animals in sheep house leads to the accumulation of microbial aerosols in sheep house. It is an important prerequisite to grasp the characteristics of bacteria in aerosols in sheep house to solve the problems of air pollution and disease prevention and control in sheep house. In this study, the microorganisms present in the air of sheep houses were investigated to gain insights into the structure of bacterial communities and the prevalence of pathogenic bacteria. Samples from six sheep pens in each of three sheep farms, totaling 18, were collected in August 2022 from Ningxia province, China. A high-volume air sampler was utilized for aerosol collection within the sheep housing followed by DNA extraction for 16S rRNA sequencing. Employing high-throughput 16S rRNA sequencing technology, we conducted an in-depth analysis of microbial populations in various sheep pen air samples, enabling us to assess the community composition and diversity. The results revealed a total of 11,207 operational taxonomic units (OTUs) within the bacterial population across the air samples, encompassing 152 phyla, 298 classes, 517 orders, 853 families, 910 genera, and 482 species. Alpha diversity and beta diversity analysis indicated that differences in species diversity, evenness and coverage between different samples. At the bacterial phylum level, the dominant bacterial groups are Firmicutes, Proteobacteria, and Actinobacteria, among which Firmicutes (97.90-98.43%) is the highest. At the bacterial genus level, bacillus, Bacteroides, Fusobacterium, etc. had higher abundance, with Bacillus (85.47-89.87%) being the highest. Through an in-depth analysis of microbial diversity and a meticulous examination of pathogenic bacteria with high abundance in diverse sheep house air samples, the study provided valuable insights into the microbial diversity, abundance, and distinctive features of prevalent pathogenic bacteria in sheep house air. These findings serve as a foundation for guiding effective disease prevention and control strategies within sheep farming environments.

Early Developmental Exposure to Triclosan Impacts Fecal Microbial Populations, IgA and Functional Activities of the Rat Microbiome.

Triclosan (TCS), a broad-spectrum antibacterial chemical, is detected in human urine, breast milk, amniotic fluid, and feces; however, little is known about its impact on the intestinal microbiome and host mucosal immunity during pregnancy and early development. Pregnant female rats were orally gavaged with TCS from gestation day (GD) 6 to postpartum (PP) day 28. Offspring were administered TCS from postnatal day (PND) 12 to 28. Studies were conducted to assess changes in the intestinal microbial population (16S-rRNA sequencing) and functional analysis of microbial genes in animals exposed to TCS during pregnancy (GD18), and at PP7, PP28 and PND28. Microbial abundance was compared with the amounts of TCS excreted in feces and IgA levels in feces. The results reveal that TCS decreases the abundance of Bacteroidetes and Firmicutes with a significant increase in Proteobacteria. At PND28, total Operational Taxonomic Units (OTUs) were higher in females and showed correlation with the levels of TCS and unbound IgA in feces. The significant increase in Proteobacteria in all TCS-treated rats along with the increased abundance in OTUs that belong to pathogenic bacterial communities could serve as a signature of TCS-induced dysbiosis. In conclusion, TCS can perturb the microbiome, the functional activities of the microbiome, and activate mucosal immunity during pregnancy and early development.

Massively parallel single-cell sequencing of diverse microbial populations.

Single-cell genetic heterogeneity is ubiquitous in microbial populations and an important aspect of microbial biology; however, we lack a broadly applicable and accessible method to study this heterogeneity in microbial populations. Here, we show a simple, robust and generalizable method for high-throughput single-cell sequencing of target genetic loci in diverse microbes using simple droplet microfluidics devices (droplet targeted amplicon sequencing; DoTA-seq). DoTA-seq serves as a platform to perform diverse assays for single-cell genetic analysis of microbial populations. Using DoTA-seq, we demonstrate the ability to simultaneously track the prevalence and taxonomic associations of >10 antibiotic-resistance genes and plasmids within human and mouse gut microbial communities. This workflow is a powerful and accessible platform for high-throughput single-cell sequencing of diverse microbial populations.

Metagenomes reveal the effect of crop rotation systems on phosphorus cycling functional genes and soil phosphorus avail–ability

The use of different cropping systems affects soil phosphorus (P) availability. Microbes play a main role in regulating soil P cycling. Currently, there is a knowledge gap on the effects of the long-term use of different crop rotation systems on microbial functional genes involved in P cycling on soil P availability. In this study, metagenomics was used to determine microbial functional genes involved in P cycling in a 12-year experiment that included three crop rotation systems: wheat–maize rotation (WM), wheat–cotton rotation (WC), and wheat–soybean rotation (WS). WS had a significantly higher AP content than WC (37.3%) and WM (41.5%). Further analysis of the soil microbial population showed that WS mainly enriched the abundance of Proteobacteria, Actinobacteria, and Firmicutes from the phylum to genus levels. For the P-cycling genes, WS significantly increased the P-cycling gene abundance of organic P mineralization (phoD, phnA, and phnP) compared with WC and WM. WC enhanced the microbial function of the Inorganic P solubilization genes gcd and gppa. WM enhanced the function of polyphosphate degradation, and the abundance of genes spoT and ppnK was significantly increased in WM soil compared with WC and WS soil. In addition, our structural equation model and network analysis showed that the organic P mineralization gene abundance had a significant effect on the available P content; the effect coefficients were 0.73, and the organic P mineralization genes phoD, phnA, and phnP, which were enriched in WS soil, were keystone genes in the process of increasing the soil-available P. Our results highlight the relationship between P cycle functions and cropping systems, which also has implications for enhancing P availability through the use of different crop systems in agricultural production.

Microbial Population Analysis Based on 16S rRNA Detection and Its Application in Epidemic Disease Warning

Microbial Population Analysis Based on 16S rRNA Detection and Its Application in Epidemic Disease Warning

Human gut microbiota and endocrinology: paradigm shift from genome to its regulation.

Over the last two decades, it has become clear that the human gut microbiota, a complex community of bacteria, archaea, fungi and viruses, are a critical determinant of human health and disease. Microbiota-derived metabolites provide the host with energy, protect against pathogens, modulate immune and endocrine systems as well as the level of reactive oxygen species in the gut. It has come with no surprise that the human gut microbiota is also linked to the production, utilisation and regulation of host hormones. This implies that the gut microbiota is capable of influencing human behaviour, appetite regulation and metabolism as well as development and immunity. Many of the advances in the field of crosstalk between the gut microbiota and host health, disease and behaviours are generally based on DNA analyses of microbial populations and transplantation of monocultured commensal species to germ-free animals. Recent reports on the activity of the gut microbiota in gastrointestinal diseases such as inflammatory bowel disease and colorectal cancer have highlighted two important points. First, microbial DNA-based abundance does not always correlate with their level of activity and secondly, that metabolism of the complex gut microbiota is regulated by host health status, including the production and metabolism of several human hormones. In this review, we will discuss the lessons learnt from studying the activity and metabolism of the human gut microbiota in health and across gastrointestinal diseases, and how these findings can shape future research on the microbiome-gut-endocrine axis.

Analysis of Soil Microbial Activity and Population in Rhizosphere Soil Exposed to Chlorpyrifos

Chlorpyrifos (CPF) is a popular organophosphorus pesticide that is widely employed in agricultural activities. However, we lack information regarding the relationship between soil microbial activity and population under CPF influence, which prohibits us from measuring CPF's actual impact on soil. In the present study, the effect of chlorpyrifos on soil microbial activity was assessed in an indoor pot experiment. The fertile soil was treated with 500 ppm of commercial-grade chlorpyrifos and paddy seedlings were transplanted. The soils treated with bacterial inoculants showed an increased microbial population on the 30th day after inoculation compared to soil receiving sole chlorpyrifos treatment. The same trend was followed on the 60th &amp; 90th day as well. The combination of inoculants resulted in a maximum increase in the population compared to the single inoculants. As a result, there was an increase in soil enzymatic activities viz. dehydrogenase and phosphatase. Thus, inoculating the pesticide-degrading bacteria would lessen the detrimental effects of pesticides on the soil health.

Enhancing Anaerobic Digestion with an UASB Reactor of the Winery Wastewater for Producing Volatile Fatty Acid Effluent Enriched in Caproic Acid

The production of Volatile Fatty Acids (VFAs) from wastewater holds significant importance in the context of biorefinery concepts due to their potential as valuable precursors for various bio-based processes. Therefore, the primary objective of this research is to investigate the fermentation of Winery Wastewater (WW) in an Upflow Anaerobic Sludge Blanket (UASB) reactor to generate VFAs, with particular emphasis on Caproic Acid (HCa) production and the dynamics of the microbiota, under varying Hydraulic Retention Time (HRT) periods (8, 5, and 2.5 h). The change from an 8 h to a 5 h HRT period resulted in an approximately 20% increase in total VFA production. However, when the HRT was further reduced to 2.5 h, total VFA production decreased by approximately 50%. Concerning the specific production of HCa, expressed in grams of Chemical Oxygen Demand (gCOD), the maximum yield was observed at around 0.9 gCOD/L for a 5-h HRT. Microbial population analysis revealed that Eubacteria outnumbered Archaea across all HRTs. Population dynamics analysis indicated that the Firmicutes Phylum was predominant in all cases. Within this phylum, bacteria such as Clostridium kluyveri and Clostridium sp., known for their ability to produce HCa, were identified. Based on the results obtained, the application of the UASB reactor for WW treatment, within the biorefinery framework, has the potential to provide a practical alternative for HCa production when operated with a 5 h HRT.

Microbiomics and volatile metabolomics-based investigation of changes in quality and flavor of oat (Avena sativa L.) silage at different stages.

This study aimed to analyze the fermentation quality, microbial community, and volatile metabolites of oat silage harvested at two different stages, while examining the correlation between microorganisms and volatile metabolites. Oats were harvested at two growth stages (pre-heading [PRH] and post-heading [POH] stages), followed by 90 days of natural fermentation, with 6 replicates per treatment. Pre- and post-silage samples were randomly selected for nutrient composition, fermentation parameters, microbial population, and high-throughput sequencing analysis. Volatile metabolomics analysis was also performed on samples after 90 days of fermentation to detect differences in flavor quality after silage. The effect of growth stage on the nutrient content of oats was significant, with pre-heading oats having higher crude protein and post-heading oats having higher water soluble carbohydrates content (p < 0.05). Following a 90-day fermentation period, the pH and ammonia nitrogen/total nitrogen levels in the PRH-90 (silage from pre-heading oats after 90 days of fermentation) group demonstrated a significant decrease (p < 0.05), whereas the lactic acid content was notably higher compared to the POH-90 (silage from post-heading oats after 90 days of fermentation) group (p <0.05). Lactiplantibacillus dominated in the PRH-90 group and Enterococcus dominated in the POH-90 group, with abundances of (> 86%) and (> 87%), respectively. The differential volatile metabolites of the two treatment groups were dominated by esters and terpenoids, and the differences in flavor were mainly concentrated in sweet, green, and fruity odors. The results of Kyoto encyclopedia of genes and genomes pathway enrichment analysis demonstrated three major metabolic pathways: phenylpropanoid biosynthesis, phenylalanine metabolism, and biosynthesis of secondary metabolites. Specific microorganisms were significantly correlated with flavor indicators and flavor metabolites. Lactiplantibacillus was significantly positively correlated with flavor substances indicating sweet and fruity flavors, contributing to good flavor, while Enterococcus was significantly and positively correlated with flavor substances indicating bad flavors. In summary, growth stage had significant effects on nutritional components, fermentation parameters and flavor quality of oats, with the fermentation process dominated by Lactiplantibacillus leading to good flavor, while the fermentation process dominated by Enterococcus led to the development of poor flavor.

Quantitative analysis of rhizosphere microbial population obtained from main-croplands in South Sulawesi

The study aims to investigate microbial species and quantify population richness associated with main crop rhizosphere in South Sulawesi. Survey was conducted in two areas including healthy and infected croplands. In each area about 1 ha, samples were collected to consist of 250 g bulk soil of rhizosphere in healthy and infected farms 1 month after transplanting. For analysis, those samples were carried out at the Plant pathology Lab, Department Plant Pest and Disease, Faculty of Agriculture. 10 g bulk soil separation out of 250 g obtained from rhizosphere was sterilized into water 25 mL and sieved 50-100 mesh prior to transfer to growth medium. After that, 4 % (g/mL) potato dextrose agar (PDA) in the petri dish was earlier prepared. The soil mixture (1g/10 mL) was diluted and transferred into a series dilution and parallelly loaded into solid media kept in dark room with at room temperature. Microbiota successfully growing in the solid media were split and transferred into petridish contained PDA for morphological identification and quantified through a series dilution. The study found 23 native fungal isolates consisting of Genera: Rhizopus sp. Phytophthora sp., Fusarium sp., Rhizoctonia sp., Geotrichum, Aspergillus sp., Gliocladium sp., Gongronella sp., and 14 unknown groups of fungi. Three bacterial isolates were discovered as gram-positive bacteria (GPB) in the infected cropland and the other two were gram-negative bacteria (GNB) found in healthy farm. The finding evidenced that population of microbiota ‘bacterial and fungal’ richness was twofold much higher in the healthy farm than infected farm. Bacterial population was the highest in both healthy and infected farms. There is a tendency of the higher fungal population richness, the lower rice disease incidence in croplands, vice versa.

Systemic Analysis of the Spatiotemporal Changes in Multi‐Species Electroactive Biofilms to Clarify the Gradual Decline of Current Generation in Microbial Anodes

AbstractThe decrease in the electrochemical activity of multi‐species microbial anodes in bioelectrochemical systems is the main bottleneck to overcome for bringing these technologies one‐step closer to the industrialization stage. In this study, microsized stainless steel electrodes were implemented to investigate the distinctive electrochemical behavior of salt marsh electroactive biofilms (EABs). Four main temporal stages of biocolonization and electrochemical activity were thoroughly described. Maximum biofilm growth rate, high viability and high extracellular protein matrix content favored the increasing electrochemical activity of the EAB up to its maximum current peak. Then, when gradual fall in current became irreversible, biofilm growth rate decreased together with dead cells accumulation and an increase for extracellular polysaccharides. In addition, analyses of microbial populations showed a shift from Marinobacterium spp. to Desulfuromonas spp. These findings suggest a chemical and microbial temporal evolution of the EAB, which can be directly correlated to the electrochemical performance of the bioanode.

Analysis of oral microbiota in non-vital teeth and clinically intact external surface from patients with severe periodontitis using Nanopore sequencing: a case study

ABSTRACT Periodontal diseases include a wide range of pathological conditions, damaging the supporting structures of the teeth. Origin and propagation of periodontal disease is believed to be caused by dysbiosis of the commensal oral microbiota. The aim of this study was to evaluate the presence of bacteria in the pulp cavity of teeth with severe periodontal disease with clinically intact external surface. Periodontal (P) and endodontic (E) tissue samples of root canals from six intact teeth of three patients were sampled for analysis of microbial population using Nanopore technology. Streptococcus was the predominant genus in E samples. Porphyromonas (33.4%, p = 0.047), Tannerella (41.7%, p = 0.042), and Treponema (50.0%, p = 0.0064) were significantly more present in P than in E samples. Some samples (E6 and E1) exhibited a remarkable difference in terms of microbial composition, whilst Streptococcus was a common signature in samples E2 to E5, all which were obtained from the same patient. In conclusion, bacteria were identified on both the root surface and the root canal system, thus demonstrating the possibility of bacteria to spread directly from the periodontal pocket to the root canal system even in the absence of crown’s loss of integrity.

Microbiome analysis and biocontrol bacteria isolation from rhizosphere soils associated with different sugarcane root rot severity.

To explore the causal pathogen and the correlated rhizosphere soil microecology of sugarcane root rot, we sampled the sugarcane root materials displaying different disease severity, and the corresponding rhizosphere soil, for systematic root phenotype and microbial population analyses. We found that with increased level of disease severity reflected by above-ground parts of sugarcane, the total root length, total root surface area and total volume were significantly reduced, accompanied with changes in the microbial population diversity and structure in rhizosphere soil. Fungal community richness was significantly lower in the rhizosphere soil samples from mildly diseased plant than that from either healthy plant, or severely diseased plant. Particularly, we noticed that a peculiar decrease of potential pathogenic fungi in rhizosphere soil, including genera Fusarium, Talaromyces and Neocosmospora, with increased level of disease severity. As for bacterial community, Firmicutes was found to be of the highest level, while Acidobacteria and Chloroflexi of the lowest level, in rhizosphere soil from healthy plant compared to that from diseased plant of different severity. FUNGuild prediction showed that the proportion of saprophytic fungi was higher in the rhizosphere soil of healthy plants, while the proportion of pathogenic fungi was higher in the rhizosphere soil of diseased plants. By co-occurrence network analysis we demonstrated the Bacillus and Burkholderia were in a strong interaction with Fusarium pathogen(s). Consistently, the biocontrol and/or growth-promoting bacteria isolated from the rhizosphere soil were mostly (6 out of 7) belonging to Bacillus and Burkholderia species. By confrontation culture and pot experiments, we verified the biocontrol and/or growth-promoting property of the isolated bacterial strains. Overall, we demonstrated a clear correlation between sugarcane root rot severity and rhizosphere soil microbiome composition and function, and identified several promising biocontrol bacteria strains with strong disease suppression effect and growth-promoting properties.

Degradation properties of fulvic acid and its microbially driven mechanism from a partial nitritation bioreactor through multi-spectral and bioinformatic analysis

This study employed multispectral techniques to evaluate fulvic acid (FA) compositional characteristic and elucidate its biodegradation mechanisms during partial nitritation (PN) process. Results showed that FA removal efficiency (FRE) decreased from 90.22 to 23.11% when FA concentrations in the reactor were increased from 0 to 162.30 mg/L, and that molecular size, degree of aromatization and humification of the effluent FA macromolecules all increased after treatment. Microbial population analysis indicated that the proliferation of the Comamonas, OLB12 and Thauera exhibit high FA utilization capacity in lower concentrations (<50.59 mg/L), promoting the degradation and removal of macromolecular FA. In addition, the sustained increase in external FA may decrease the abundance of above functional microorganisms, resulting in a rapid drop in FRE. Furthermore, from the genetic perspective, the elevated FA levels restricted carbohydrate (ko00620, ko00010 and ko00020) and nitrogen (HAO, AMO, NIR and NOR) metabolism-related pathways, thereby impeding FA removal and total nitrogen loss associated with N2O emissions.