Abundance Of Bacterial Species Research Articles

Long-term fertilization has different impacts on bacterial communities and phosphorus forms in sugarcane rhizosphere and bulk soils under low-P stress.

The application of phosphorus (P) fertilizer effectively improves soil P availability, but it also affects soil microbial communities. However, the responses of soil bacterial communities and P forms to long-term P fertilization, and the relationships of bacterial communities with soil P forms remain unclear in P-deficient field. In this study, the impacts of different P fertilization treatments (chemical nitrogen and potassium (NK); chemical N, P and K (NPK); and NPK plus straw (NPKS)) on the bacterial communities and P forms in sugarcane rhizosphere (RS) and bulk soils (BS) were evaluated. Compared with the NK, the NPK and NPKS treatments significantly (P<0.05) increased the yield and quality characters of sugarcane, especially under NPKS. Additionally, P fertilization significantly increased the available P (AP), soluble inorganic P (Pi) and retained Pi in both the RS and BS, but they significantly increased the Chao1 and Shannon index only in the BS; and almost all these indices were significantly higher in the RS than in the BS. The bacterial community compositions were also significantly altered by P fertilization, with major changes in the RS and minor changes in the BS. The bacterial genera that were enriched in the sugarcane rhizosphere mainly included Bradyrhizobium, Rhodanobacter, Pseudolabrys, Conexibacter, and Burkholderia-Caballeronia-Paraburkholderia, some of which potentially promote the plant growth. Compared to NK, functional groups involved in the cycling of carbon, N, and sulfur significantly increased or decreased with fertilizer P application. Moreover, the relative abundances of many bacterial species were significantly correlated with the soil P forms. In conclusion, long-term P fertilization altered bacterial structure and functions in P-deficient sugarcane soil, which could help the soil P cycling and suppling. The results provide useful information to stimulate the power of the microbes by fertilization measures to improve soil nutrients and crop production.

Investigating genetic diversity within the most abundant and prevalent non-pathogenic leaf-associated bacteria interacting with Arabidopsis thaliana in natural habitats.

Microbiota modulates plant health and appears as a promising lever to develop innovative, sustainable and eco-friendly agro-ecosystems. Key patterns of microbiota assemblages in plants have been revealed by an extensive number of studies based on taxonomic profiling by metabarcoding. However, understanding the functionality of microbiota is still in its infancy and relies on reductionist approaches primarily based on the establishment of representative microbial collections. In Arabidopsis thaliana, most of these microbial collections include one strain per OTU isolated from a limited number of habitats, thereby neglecting the ecological potential of genetic diversity within microbial species. With this study, we aimed at estimating the extent of genetic variation between strains within the most abundant and prevalent leaf-associated non-pathogenic bacterial species in A. thaliana located south-west of France. By combining a culture-based collection approach consisting of the isolation of more than 7,000 bacterial colonies with an informative-driven approach, we isolated 35 pure strains from eight non-pathogenic bacterial species. We detected significant intra-specific genetic variation at the genomic level and for growth rate in synthetic media. In addition, significant host genetic variation was detected in response to most bacterial strains in in vitro conditions, albeit dependent on the developmental stage at which plants were inoculated, with the presence of both negative and positive responses on plant growth. Our study provides new genetic and genomic resources for a better understanding of the plant-microbe ecological interactions at the microbiota level. We also highlight the need of considering genetic variation in both non-pathogenic bacterial species and A. thaliana to decipher the genetic and molecular mechanisms involved in the ecologically relevant dialog between hosts and leaf microbiota.

Untangling the link between the human gut microbiota composition and the severity of the symptoms of the COVID-19 infection.

Recent pandemic infection caused by SARS‐CoV‐2 (COVID‐19) led the scientific community to investigate the possible causes contributing to the physiopathology of this disease. In this context, analyses of the intestinal microbiota highlighted possible correlation between host‐associated bacterial communities and development of the COVID‐19. Nevertheless, a detailed investigation of the role of the human microbiota in the severity of the symptoms of this disease is still lacking. This study performed a comprehensive meta‐analysis of 323 faecal samples from public and novel Italian data sets based on the shotgun metagenomic approach. In detail, the comparative analyses revealed possible differences in the microbial biodiversity related to the individual health status, highlighting a species richness decrease in COVID‐19 patients with a severe prognosis. Moreover, healthy subjects resulted characterized by a higher abundance of protective and health‐supporting bacterial species, while patients affected by COVID‐19 disease displayed a significant increase of opportunistic pathogen bacteria involved in developing putrefactive dysbiosis. Furthermore, prediction of the microbiome functional capabilities suggested that individuals affected by COVID‐19 subsist in an unbalanced metabolism characterized by an overrepresentation of enzymes involved in the protein metabolism at the expense of carbohydrates oriented pathways, which can impact on disease severity and in excessive systemic inflammation.

S10.3c Clinical studies provide new insights on the association between the microbiota and host resistance to Candida albicans intestinal colonization

S10.3 The mycobiome characterization: future perspectives or just a trend?, September 24, 2022, 10:30 AM - 12:00 PM Objectives Candida albicans is both a harmless commensal intestinal yeast in healthy individuals and a harmful opportunistic pathogen in immunocompromised patients, causing life-threatening invasive candidiasis. C. albicans intestinal overgrowth is a prerequisite for intestinal translocation, which is at the root of invasive candidiasis. Therefore, to prevent invasive candidiasis in immunocompromised patients, it is necessary to curb intestinal C. albicans overgrowth. However, little is known of the role of bacterial species of the microbiota in dampening C. albicans intestinal colonization.We aimed to decipher the influence of the bacterial and fungal intestinal microbiota on C. albicans gut colonization in healthy individuals in whom their microbiota was modified or not by antibiotic treatment.MethodsWe studied two cohorts of healthy individuals: the first cohort included 22 volunteers for which fecal samples were collected before, during and after a 3-day regimen of third-generation cephalosporin antibiotics. The second cohort gathered 1000 healthy individuals for which a single fecal sample was collected. We quantified C. albicans carriage using a specific quantitative PCR approach. We monitored the antibiotic effect on the composition of the fungal microbiota—the so called mycobiota—in the gut of the individuals up to 180 days post-antibiotic exposure, using both the qPCR data and ITS1 targeted metagenomic. We also monitored the level of fecal β-lactamase activity, which is known to modulate the intensity of post-cephalosporin intestinal dysbiosis. Finally, to identify potential C. albicans inhibiting bacteria, we used MaAsLin2 to search for associations between C. albicans levels and bacterial species abundance, deduced from shotgun metagenomics data obtained from all individuals and annotated at the species level.ResultsA very high level of C. albicans carriage was observed in both cohorts, with a prevalence of 95.2% and 83.1% in the first and second cohort, respectively. Yet, the quantity of C. albicans DNA detected varied greatly between subjects. The mycobiota composition was significantly altered by antibiotics and the fungal load was increased both at short and long term. Particularly, C. albicans abundance was increased but with wide inter-subject variations. A part of these variations was explained by changes in the levels of endogenous fecal β-lactamase activity, with subjects characterized by a low increase of β-lactamase activity displaying a higher increase of C. albicans levels. Finally, using shotgun metagenomics data, we identified a first set of 50 bacterial and archaeal species whose abundance inversely correlated with C. albicans abundance.ConclusionThese results (1) bring a new understanding of C. albicans overgrowth in healthy individuals, (2) lead to the identification of microbial signatures with a potential key role in controlling C. albicans gut colonization, and finally (3) show for the first time that changes in endogenous fecal β-lactamase activity is a key factor for C. albicans overgrowth in the gut after antibiotic exposure. Taken together, these results open the way for new intervention strategies to curb C. albicans intestinal overgrowth.

High-Throughput Sequencing Investigation of Bacterial Diversity in Chronic Suppurative Otitis Media and Middle Ear Cholesteatoma.

Background Chronic otitis media is a common middle ear disease in otolaryngology. Bacterial infection is considered as the cause of the disease, but relying on conventional bacterial cultures can be problematic for identifying specific pathogens. Current research suggests that bacteria in microbial communities can only be identified by rDNA sequencing of bacteria. Methods This cross-sectional study utilized broad-range PCR amplification of 16S rRNA genes with clone analysis to compare bacterial diversity in lesions from 6 patients with chronic suppurative otitis media (CSOM) and 10 patients with cholesteatoma of middle ear lesions. Bacteria were analyzed at the levels of phylum, order, family, genus, and species. Results The age and sex difference between the patients with chronic suppurative otitis media and the patients with middle ear cholesteatoma were comparable (P > 0.05). Bacterial species abundance and species diversity were greater in cholesteatoma of the middle ear lesions than in CSOM lesions. The total number of detected operational taxonomic units (OTU) was 838, comprising 788 OTU detected in cholesteatoma pathological tissues, 230 in CSOM pathological tissues, and 180 OTU common to both groups. Proteus is a major part of CSOM (99.46%, P = 0.000321). The phyla detected in the Cholesteatoma samples were Proteus (Proteobacteria) (35.77%), thikum (Firmicutes) (44.21%, P = 0.001071), and Actinomycetes (Actinobacteria) (16.66%, P = 0.032464). At all bacterial taxonomic levels, the epithelial tissue of middle ear cholesteatoma was complex in terms of bacterial diversity, covering many Gram-positive and Gram-negative bacteria, likely related to bacterial microbiome formation. In contrast, the bacteriology of the CSOM lesions was relatively simple at all taxonomic levels, with all sequences characterized as belonging to Gram-negative bacteria. Conclusion Our results suggest that persistent middle ear cholesteatoma infection may be a microbial flora disorder related to conditional pathogenic bacteria rather than a single bacterial infectious disease. The pathogen is relatively single in the diseased tissue of chronic suppurative otitis media, which is the main reason for its effective antiinfection treatment.

Temporal Dynamics of Rare and Abundant Soil Bacterial Taxa from Different Fertilization Regimes Under Various Environmental Disturbances.

ABSTRACTGlobal climate change has emerged as a critical environmental problem. Different types of climate extremes drive soil microbial communities to alternative states, leading to a series of consequences for soil microbial ecosystems and related functions. An effective method is urgently needed for buffering microbial communities to tackle environmental disturbances. Here, we conducted a series of mesocosm experiments in which the organic (NOF) and chemical fertilizer (NCF) long-term-amended soil microbiotas were subjected to environmental disturbances that included drought, flooding, freeze-thaw cycles, and heat. We subsequently tracked the temporal dynamics of rare and abundant bacterial taxa in NOF and NCF treatment soils to assess the efficiencies of organic amendments in recovery of soil microbiome. Our results revealed that freeze-thaw cycles and drought treatments showed weaker effects on bacterial communities than flooding and heat. The turnover between rare and abundant taxa occurred in postdisturbance succession of flooding and heat treatments, indicating that new equilibria were tightly related to the rare taxa in both NCF and NOF treatment soils. The Bayesian fits of modeling for the microbiome recovery process revealed that the stability of abundant taxa in NOF was higher than that in NCF soil. In particular, the NOF treatment soil reduced the divergence from the initial bacterial community after weak perturbations occurred. Together, we demonstrated that long-term organic input is an effective strategy to enhance the thresholds for transition to alternative states via enhancing the stability of abundant bacterial species. These findings provide a basis for the sustainable development of agricultural ecosystems in response to changing climates.IMPORTANCE Different climate extremes are expected to be a major threat to crop production, and the soil microbiome has been known to play a crucial role in agricultural ecosystems. In recent years, we have known that organic amendments are an effective method for optimizing the composition and functioning of the soil microbial community and maintaining the health of the soil ecosystem. However, the effects of organic fertilization on buffering bacterial communities against environmental disturbances and the underlying mechanisms are still unclear. We conducted a series of mesocosm experiments and showed that organic fertilizers had additional capacities in promoting the soil microbiome to withstand climate change effects. Our study provides both mechanistic insights as well as a direct guide for the sustainable development of agricultural ecosystems in response to climate change.

Effect of continuous cropping of konjac (Amorphophallus konjac) on soil bacterial communities as evaluated by Illumina high-throughput sequencing

ABSTRACT Illumina high-throughput sequencing was used to explore the diversity and composition of the soil and root endosphere bacterial communities in three replanted konjac sites in 1-, 3-, and 5-year cropping systems. Continuous cropping of konjac caused a substantial decrease in soil pH and the activities of soil sucrase, urease, catalase, and alkaline phosphatase, and led to a remarkable and persistent decrease in the soil and root endosphere bacterial species abundance and alpha-diversity. Among the nine dominant bacterial phyla, Proteobacteria and Actinobacteria had the highest relative abundance, with averages of 61.3% and 11.2%, respectively. Several potentially beneficial genera, including Acinetobacter, Arthrobacter, and Pseudomonas, were less abundant in soil (84.6%, 82.7%, and 83.3%) and root (98.6%, 71.4%, and 98.1%) samples under 5 years of continuous cropping compared with those under 1-year cropping. Conversely, the potentially harmful genus Haliangium exhibited higher relative abundance in 5-year soil and root samples than in 1-year samples. Continuous cropping altered the bacterial community composition in the soil and root endosphere of konjac by influencing soil variables, leading to a reduction in the alpha-diversity of bacteria and the relative abundance of potentially beneficial bacteria, which in turn resulted in konjac poor growth in the continuous cropping system.

Assessing the effect of antihypertensives on plaque microbiota in patients with periodontitis and hypertension using 16S rRNA sequencing: A cross-sectional study.

Periodontitis is initiated or accelerated by dysbiosis of oral microorganisms. When hypertension is accompanied in periodontitis patients, changes of oral microbiota occur. Since there are no reports on antihypertensives, we assessed their effect on the oral microbial profiles of patients with periodontitis. This study involved 95 participants divided into two groups: those with periodontitis and hypertension (P_HT), and those with periodontitis and taking medications for hypertension (P_mHT). Plaque samples were collected from the buccal, supragingival, and subgingival sites of the oral cavities of these patients. DNA was extracted, and the V3-V4 region of the 16S ribosomal RNA was sequenced and analyzed. The P_HT and P_mHT groups were similar with respect to the alpha- and beta-diversity as well as the dominant phyla and genera, but differed in the relative abundance of bacterial species (85 species). In the P_mHT group, the relative abundance of major periodontal pathogens was greatly increased. In particular, Tannerella forsythia, Treponema denticola, and Fretibacterium fastidiosum increased nearly three times in the linear discriminant analysis score in the supragingival plaque. Also, there was an increase in the relative abundance of Prevotella spp., associated with periodontitis and nitrate reduction, which was also evident in the supragingival plaque. These findings indicate that antihypertensives induce dysbiotic changes in the oral microbiota of patients with periodontitis, which are associated with increases in the relative abundance of periodontal pathogens. Therefore, more active periodontal treatment and supportive periodontal therapy are required in patients taking antihypertensives.

The Resistome of ESKAPEE Pathogens in Untreated and Treated Wastewater: A Polish Case Study.

The aim of this study was to quantify ESKAPEE bacteria, genes encoding resistance to antibiotics targeting this group of pathogens, as well as integrase genes in municipal wastewater and river water. Environmental DNA was extracted from the collected samples and used in deep sequencing with the Illumina TruSeq kit. The abundance of bacterial genera and species belonging to the ESKAPEE group, 400 ARGs associated with this microbial group, and three classes of integrase genes were determined. A taxonomic analysis revealed that Acinetobacter was the dominant bacterial genus, whereas Acinetobacter baumannii and Escherichia coli were the dominant bacterial species. The analyzed samples were characterized by the highest concentrations of the following ARGs: blaGES, blaOXA-58, blaTEM, qnrB, and qnrS. Acinetobacter baumannii, E. coli, and genes encoding resistance to β-lactams (blaVEB-1, blaIMP-1, blaGES, blaOXA-58, blaCTX-M, and blaTEM) and fluoroquinolones (qnrS) were detected in samples of river water collected downstream from the wastewater discharge point. The correlation analysis revealed a strong relationship between A. baumannii (bacterial species regarded as an emerging human pathogen) and genes encoding resistance to all tested groups of antimicrobials. The transmission of the studied bacteria (in particular A. baumannii) and ARGs to the aquatic environment poses a public health risk.

A widely distributed genus of soil Acidobacteria genomically enriched in biosynthetic gene clusters

Bacteria of the phylum Acidobacteria are one of the most abundant groups across soil ecosystems, yet they are represented by comparatively few sequenced genomes, leaving gaps in our understanding of their metabolic diversity. Recently, genomes of Acidobacteria species with unusually large repertoires of biosynthetic gene clusters (BGCs) were reconstructed from grassland soil metagenomes, but the degree to which species with this trait are widespread is still unknown. To investigate this, we assembled 46 metagenome-assembled genomes recovered from permanently saturated organic-rich soils of a vernal (spring) pool ecosystem in Northern California. We obtained high and medium-quality draft genomes for three novel species from Candidatus Angelobacter (a proposed subdivision 1 Acidobacterial genus), a genus that is genomically enriched in genes for specialized metabolite biosynthesis. Acidobacteria were particularly abundant in the vernal pool sediments, and a Ca. Angelobacter species was the most abundant bacterial species detected in some samples. We identified numerous diverse biosynthetic gene clusters in these genomes, and also in five additional genomes from other publicly available soil metagenomes for other related Ca. Angelobacter species. Metabolic analysis indicates that Ca. Angelobacter likely are aerobes that ferment organic carbon, with potential to contribute to carbon compound turnover in soils. Using metatranscriptomics, we identified in situ metabolic activity and expression of specialized metabolic traits for two species from this genus. In conclusion, we expand genomic sampling of the uncultivated Ca. Angelobacter, and show that they represent common and sometimes highly abundant members of dry and saturated soil communities, with a high degree of capacity for synthesis of diverse specialized metabolites.

Antimicrobial Resistance and Associated Risk Factors of Gram-Negative Bacterial Bloodstream Infections in Tikur Anbessa Specialized Hospital, Addis Ababa.

BackgroundBloodstream infections (BSIs) are significant causes of morbidity and mortality in Ethiopia and worldwide. Alarming is the rapid global spread of antimicrobial resistance (AMR) in bacteria.ObjectiveTo determine the microbial profile, antimicrobial susceptibility pattern, and associated risk factors for bloodstream infections in Tikur Anbessa Specialized Hospital (TASH) Addis Ababa Ethiopia.MethodsA cross-sectional study was conducted between September 2018 and March 2019. Blood collected twice from each septicemia suspected patient were processed following standard bacteriological procedures. AST was performed by using the disk diffusion test according to CLSI 2017 and 2018 guidelines. Data captured in Epidata were cleaned and analyzed by SPSS version 21 software.ResultsThe prevalence of BSI was 28.06% and a higher proportion of pathogene detected were gram-negative bacteria (GNB) (54.5%) and gram-positive bacteria (GPB) (45.43%). The most abundant bacterial species were Klebsiella pneumoniae 17.6%, CoNS 15.2%, and Acinetobacter spp 11.0%. Culture positivity was associated with age below 6 years, neonates AOR p=<0.001, infants AOR p=<0.001, Pre-school P=0.002, ICU admission COR p=<0.001, length of admission >5 days COR P=0.016, temperature greater than 38°C, AOR p=0.013, instrument usage during medical care AOR, p=<0.001, chronic illness AOR p=0.027, and neonatal incubation AOR p=0.013. GNB average drug resistance rate was 57.9% of the commonly used antibiotics and the most efficient and inefficient drugs were amikacin (10.8%) and ampicillin (94.6%). The gram-negative isolates showed a 95.3% rate of multi-drug resistance; and MDR, XDR, and PDR were observed at 55.8%, 32.2%, and 7.3%, of isolates respectively. This finding shows children especially neonates were highly affected by drug resistant BSI.ConclusionPediatric patients and ICU patients are more affected by BSI, and drug-resistant bacteria are a major problem. Therefore, appropriate intervention approaches need to be implemented.

Suppression of Midgut Microbiota Impact Pyrethroid Susceptibility in Aedes aegypti.

Aedes aegypti is a mosquito that transmits viral diseases such as dengue, chikungunya, Zika, and yellow fever. The insect’s microbiota is recognized for regulating several biological processes, including digestion, metabolism, egg production, development, and immune response. However, the role of the bacteria involved in insecticide susceptibility has not been established. Therefore, the objective of this study was to characterize the resident microbiota in a field population of A. aegypti to evaluate its role associated with susceptibility to the insecticides permethrin and deltamethrin. Mosquitoes were fed 10% sucrose mixed with antibiotics and then exposed to insecticides using a diagnostic dose. DNA was extracted, and sequencing of bacterial 16S rRNA was carried out on Illumina® MiSeq™. Proteobacteria (92.4%) and Bacteroidetes (7.6%) were the phyla, which are most abundant in mosquitoes fed with sucrose 10%. After exposure to permethrin, the most abundant bacterial species were Pantoea agglomerans (38.4%) and Pseudomonas azotoformans-fluorescens-synxantha (14.2%). Elizabethkingia meningoseptica (38.4%) and Ps. azotoformans-fluorescens-synxantha (26.1%) were the most abundant after exposure to deltamethrin. Our results showed a decrease in mosquitoes’ survival when exposed to permethrin, while no difference in survival when exposed to deltamethrin when the microbiota was modified. We found that the change in microbiota modifies the response of mosquitoes to permethrin. These results are essential for a better understanding of mosquito physiology in response to insecticides.

Metagenomic Sequencing of the Gallbladder Microbiome: Bacterial Diversity Does Not Vary by Surgical Pathology

IntroductionAlterations in the microbiome contribute to the pathogenesis of many gastrointestinal diseases. However, the composition of the microbiome in gallbladder disease is not well described. MethodsWe aimed to characterize the biliary microbiome in cholecystectomy patients. Bile and biliary stones were collected at cholecystectomy for a variety of surgical indications between 2017 and 2019. DNA was extracted and metagenomic sequencing was performed with subsequent taxonomic classification using Kraken2. The fraction of bacterial to total DNA reads, relative abundance of bacterial species, and overall species diversity were compared between pathologies and demographics. ResultsA total of 74 samples were obtained from 49 patients: 46 bile and 28 stones, with matched pairs from 25 patients. The mean age was 48 years, 76% were female, 29% were Hispanic, and 29% of patients had acute cholecystitis. The most abundant species were Klebsiella pneumoniae, Staphylococcus aureus, and Streptococcus pasteurianus. The bacterial fraction in bile and stone samples was higher in acute cholecystitis compared to other non-infectious pathologies (p < 0.05). Neither the diversity nor differential prevalence of specific bacterial species varied significantly between infectious and other non-infectious gallbladder pathologies. Multivariate analysis of the non-infectious group revealed that patients over 40 years of age had increased bacterial fractions (p < 0.05). ConclusionsMetagenomic sequencing permits characterization of the gallbladder microbiome in cholecystectomy patients. Although a higher prevalence of bacteria was seen in acute cholecystitis, species and diversity were similar regardless of surgical indication. Additional study is required to determine how the microbiome can contribute to the development of symptomatic gallbladder disease.

A proteolytically activated antimicrobial toxin encoded on a mobile plasmid of Bacteroidales induces a protective response

Phocaeicola vulgatus is one of the most abundant and ubiquitous bacterial species of the human gut microbiota, yet a comprehensive analysis of antibacterial toxin production by members of this species has not been reported. Here, we identify and characterize a previously undescribed antibacterial protein. This toxin, designated BcpT, is encoded on a small mobile plasmid that is largely confined to strains of the closely related species Phocaeicola vulgatus and Phocaeicola dorei. BcpT is unusual in that it requires cleavage at two distinct sites for activation, and we identify bacterial proteases that perform this activation. We further identify BcpT’s receptor as the Lipid A-core glycan, allowing BcpT to target species of other Bacteroidales families. Exposure of cells to BcpT induces a response involving an unusual sigma/anti-sigma factor pair that is likely triggered by cell envelope stress, resulting in the expression of genes that partially protect cells from multiple antimicrobial toxins.

Resistance evolution can disrupt antibiotic exposure protection through competitive exclusion of the protective species

Antibiotic degrading bacteria can reduce the efficacy of drug treatments by providing antibiotic exposure protection to pathogens. While this has been demonstrated at the ecological timescale, it is unclear how exposure protection might alter and be affected by pathogen antibiotic resistance evolution. Here, we utilised a two-species model cystic fibrosis (CF) community where we evolved the bacterial pathogen Pseudomonas aeruginosa in a range of imipenem concentrations in the absence or presence of Stenotrophomonas maltophilia, which can detoxify the environment by hydrolysing β-lactam antibiotics. We found that P. aeruginosa quickly evolved resistance to imipenem via parallel loss of function mutations in the oprD porin gene. While the level of resistance did not differ between mono- and co-culture treatments, the presence of S. maltophilia increased the rate of imipenem resistance evolution in the four μg/ml imipenem concentration. Unexpectedly, imipenem resistance evolution coincided with the extinction of S. maltophilia due to increased production of pyocyanin, which was cytotoxic to S. maltophilia. Together, our results show that pathogen resistance evolution can disrupt antibiotic exposure protection due to competitive exclusion of the protective species. Such eco-evolutionary feedbacks may help explain changes in the relative abundance of bacterial species within CF communities despite intrinsic resistance to anti-pseudomonal drugs.

Aromatic-turmerone ameliorates DSS-induced ulcerative colitis via modulating gut microbiota in mice.

Curcuma longa L. is one of the traditional Chinese herbs in the list of medicinal and food homology. Aromatic-turmerone is the main ingredient in turmeric essential oil. The aim of the present study is to investigate the treatment of Aromatic-turmerone on DSS-included colitis and its regulatory effect on intestinal flora disorder. Male KM mice supplemented with different concentration of aromatic-turmerone and mesalazine are subjected to 2% DSS in drinking water to induce colitis. Colon and cecum contents were collected for colitis lesion evaluation and inflammation-related gene analysis and colon contents for gut microbiota. The results show that treatments with Aromatic-turmerone significantly prevents colon shortening, alleviates the damage of colonic tissue, and reduces colonic inflammatory cytokines TNF-α and COX-2. Furthermore, the 16S rDNA gene sequence data indicate that Aromatic-turmerone improve the abundance of bacterial species, maintain some beneficial bacteria, and reduce harmful bacteria. Aromatic-turmerone downregulates the colonic inflammatory cytokines and modulates the abundance of intestinal flora, which is conductive to ameliorates DSS-induced colitis. Regularly intake of the edible herb may be help to prevent ulcerative colitis-related diseases.

In vitro Effect of Alum on Microbes Associated with Foliar Phytoplasma Disease of Noni

Foliar phytoplasma disease of Noni (Morinda citrifolia) has a devastating socioeconomic impact on host crop species and a huge problem to farmers and scientists. Therefore, this study investigates the in vitro effect of alum on microorganisms associated with foliar phytoplasma disease (FPD) of Noni. Bacteria and fungi were isolated and identified by culture-dependent technique using standard microbiological procedures and susceptibility of species were evaluated by disc and agar well diffusion techniques and inhibition zones (IZs) were measured in millimeter (mm). The microbes identified were Bacillus subtilis, B. tequilensis, Brevundimonas vesicularis, B. cereus, Staphylococcus aureus and Serratia species as well as Aspergillus flavus, A. fumigatus, A. niger and Penicillium species. Relative abundance (%) of bacterial species occurred in the order; S. aureus &gt; B. tequilensis &gt; B. cereus and least being Br. vesicularis whereas fungi were A. fumigatus (75%), A. niger and A. flavus (50%) respectively and Penicillium (25%) species. Susceptibility test efficacy of Alum was concentration dependent with Serratia sp. as (6.0mm) and S. aureus (4.0mm) whilst A. flavus (36.0mm), A. fumigatus (32.5mm), Penicillium (30.2mm) and A. niger (30.0mm) at 5.0% Alum concentrations as the largest IZs respectively. The minimum inhibitory concentration (MIC) of Alum against all the microflora were &lt; 2.0gm/mL except for S. aureus which portends a good future prospects in agronomy. However, the higher concentrations of Alum compared favourably with Ketoconazole (control) but showed wide disparity with Ofloxacin (control). This study, however, may proffer solutions for the prevention and management of FPD or foliar related diseases by periodic spraying or fumigation with Alum.

P603: GUT MICROBIOME IN CHRONIC LYMPHOCYTIC LEUKEMIA SHOWS DEPLETION OF SHORT-CHAIN FATTY ACIDS PRODUCING BACTERIA

Background: Recent studies have shown extensive crosstalk between our immune system and gut microbiome (GM). The host immune system plays a vital role in the maintenance of GM homeostasis by 1) establishing a balance between eliminating invading pathogens and promoting the growth of beneficial microbes, 2) producing short-chain fatty acids (SCFA), the main source of nutrition for the colon cells, and 3) modulating the immune system by cytokine production. Mounting evidence shows that the GM of patients with high rates of infection are characterized by an imbalance of bacteria, inducing proinflammatory states and reduced capacity for SCFA synthesis. As chronic lymphocytic leukemia (CLL) is, among others, also characterized by high rate of infectious complications and an altered immune system, it is warranted to explore composition of the CLL microbiome. Aims: We aim to investigate the hypothesis that deviation of the GM from homeostasis, i.e. loss of ‘health promoting’ gut microbes and/or overgrowth of pathogenic bacteria, distinguishes patients with CLL from the background population. Methods: Feces samples of patients with CLL were collected, immediately fixated and frozen within 72 h; total genomic DNA was sequenced. Feces samples of healthy controls were chosen to match the CLL population with respect to age, demographic data, sample collection method, and sequencing platform. Taxonomical profiling was done using an in-house bioinformatics pipeline. Results: A total of 61 CLL patients and 30 healthy individuals were included in the study. We observed reduced GM alpha diversity, and depletion of bacterial members of Lachnospiraceae and Ruminococcaceae families among the CLL patients when compared to healthy individuals. Our data show that members of the Lachnospiraceae family (Anaerostipes hadrus, Coprococcus comes, Blautia spp., Dorea spp.), and 3 members of Ruminococcaeae family (Ruminococcus torques, Ruminococcus bromii, Faecalibacterium prausnitzii) were among the most differentially abundant bacterial species between the microbiomes of healthy individuals and CLL. Their mean proportions were shown to be significantly higher in healthy microbiome samples. As further differentially abundant species we observed Bacteroides sp. and Alistipes finegoldii, which both demonstrated significantly higher mean proportions in CLL microbiomes (Fig 1). Image:Summary/Conclusion: To sum up, the CLL microbiomes in comparison to healthy controls demonstrated lower enrichment of Lachnospiraceae and Ruminococcaceae families, the major SCFAs-producing bacterial taxa reported to have a protective effect against inflammation. This supports the notion that proinflammatory risk factors identified in other cohorts with GM dysbiosis are also present within CLL patients. As CLL represents an antigen driven malignancy with immune dysfunction, we hypothesize that GM dysbiosis could both be implicated in the pathogenesis of CLL, through antigenic drive, and contribute to the distortion of the immune system in CLL. Notably, both immune dysfunction and treatment (e.g. antimicrobials) may influence the CLL microbiome itself and therefore confound cross-sectional clinical studies. We therefore plan to investigate the interaction between microbiome and CLL development in the TCL1 mouse model of CLL. Also, identification of potential mechanistic links between the GM and the microenvironment in CLL should be investigated, e.g. extravesicular vesicles or cytokines released from or impacted by the GM. In addition, modulation of the microbiome in animal models may help to establish causal connections between the GM and CLL development.

Targeted Analysis of the Gut Microbiome for Diagnosis, Prognosis and Treatment Individualization in Pediatric Inflammatory Bowel Disease.

We explored the fecal microbiota in pediatric patients <18 years of age with treatment-naïve IBD (80 Crohn’s disease (CD), 27 ulcerative colitis (UC)), in 50 non-IBD patients with gastrointestinal symptoms without inflammation and in 75 healthy children. Using a targeted qPCR approach, the quantities of more than 100 different bacterial species were measured. Results: The bacterial abundance was statistically significantly reduced in the IBD and non-IBD patients compared to the healthy children for several beneficial species. The CD patients had a lower abundance of Bifidobacterium species compared to the UC patients, and the IBD patients in need of biologic therapy had a lower abundance of butyrate producing bacteria. Based on the abundance of bacterial species at diagnosis, we constructed Diagnostic, Phenotype and Prognostic Indexes. Patients with a high Diagnostic Index had 2.5 times higher odds for having IBD than those with a lower index. The CD patients had a higher Phenotype Index than the UC patients. Patients with a high Prognostic Index had 2.1 higher odds for needing biologic therapy compared to those with a lower index. Conclusions: The fecal abundance of bacterial species can aid in diagnosing IBD, in distinguishing CD from UC and in identifying children with IBD in need of biologic therapy.

Evaluation of bacterial community in constructed wetlands treating different sources of wastewater

Bacteria serve as important components of a constructed wetland (CW) system. Various bacterial communities aid in pollutant removal; however, environmental conditions and other external variables can greatly affect their performance and diversity. In this study, four constructed wetlands treating secondary livestock wastewater (LCW), agricultural runoff (ACW1 and ACW2) and urban stormwater (HCW) were investigated to evaluate the relationship between the inflow pollutants and the bacterial community. Based on the findings, the 20 dominant bacterial species in water samples collected from the livestock area (LCW) constituted 98.5% to 99.7% the total bacterial population. In the case of agricultural areas (ACW1 and ACW2), the 20 most abundant bacterial species constituted 99.7% to 99.8% of the total bacterial population. Similarly, the 20 dominant bacterial species found in the soil samples from livestock and agricultural areas made up 97.2% to 98.7% and 99.1% to 99.6% of the total bacterial population, respectively. Generally, the diversity of bacteria in soil was higher compared to water. It is important to establish a target bacterial habitat when creating CW for optimized ecological functions.