Aerobic spore-forming bacteria associated with ropy bread: Identification, characterization and spoilage potential assessment.

Aerobic spore-forming (ASF) bacteria have been reported to cause ropiness in bread. Sticky and stringy degradation, discoloration, and an odor reminiscent of rotting fruit are typical characteristics of ropy bread spoilage. In addition to economic losses, ropy bread spoilage may lead to health risks, as virulent strains of ASF bacteria are not uncommon. However, the lack of systematic approaches to quantify physicochemical spoilage characteristics makes it extremely difficult to assess rope formation in bread. To address this problem, the aim of this study was to identify, characterize and objectively assess the spoilage potential of ASF bacteria associated with ropy bread. Hence, a set of 82 ASF bacteria, including isolates from raw materials and bakery environments as well as strains from international culture collections, were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and their species identity confirmed by 16S rRNA and gyrA or panC gene sequencing. A standardized approach supported by objective colorimetric measurements was developed to assess the rope-inducing potential (RIP) of a strain by inoculating autoclaved bread slices with bacterial spores. In addition, the presence of potential virulence factors such as swarming motility or hemolysis was investigated. This study adds B. velezensis, B. inaquosorum and B. spizizenii to the species potentially implicated of causing ropy bread spoilage. Most importantly, this study introduces a standardized classification protocol for assessing the RIP of a bacterial strain. Colorimetric measurements are used to objectively quantify the degree of breadcrumb discoloration. Furthermore, our results indicate that strains capable of inducing rope spoilage in bread often exhibit swarming motility and virulence factors such as hemolysis, raising important food quality considerations.

Effect of Antibiotic Exposure on Upper Respiratory Tract Bacterial Flora.

BACKGROUND The human microbiota modulates the immune system and forms the surface flora. Antibiotic administration causes dysbiosis in the intestinal flora. It is not clear if antibiotic administration in the community effects the upper airway flora in the mid-term or long-term. This study aims to define long-term influence of antibiotics on upper airway flora. MATERIAL AND METHODS In this prospective study, aerobic microbiological analysis of nasal and nasopharyngeal surfaces was performed. Antibiotic administration history of the last 6 months was retrieved using the social insurance database. Culture results of antibiotic-treated and antibiotic-naïve subjects were compared by Pearson's chi-square test or Fisher's exact test. RESULTS A total of 210 subjects were included in the study. Normal flora were documented in 86 nasal swabs and 99 nasopharyngeal swabs. Most of the remaining cases demonstrated gram-positive bacterial overgrowth. There were 113 subjects who did not receive any antibiotic, and 93% of the remaining 97 patients received broad-spectrum antibiotics. Statistical analysis showed that nasal and nasopharyngeal flora did not change upon antibiotic administration, but antibiotic administration during the last month caused increased methicillin resistance development of coagulase-negative Staphylococcus and Staphylococcus aureus microorganisms. CONCLUSIONS Antibiotic exposure did not lead to perturbations in general composition of upper airway flora within 6 months, although the incidence of methicillin resistance in coagulase-positive and -negative Staphylococci demonstrated significant increases when patients received antibiotic during the last month. This should be considered in case of broad-spectrum antibiotic administration, since methicillin resistance increases the morbidity and mortality of nosocomial Staphylococcus infections.

Nanocristais de besifloxacino para o tratamento de conjuntivite bacteriana: preparação, caracterização físico-química e toxicidade / Besifloxacin nanocrystals for treating bacterial conjunctivitis: preparation, physicochemical characterization, and toxicity

A conjuntivite bacteriana tem significante impacto na Saúde Pública. Essa infecção representa mais de um terço das doenças oculares relatadas em âmbito global. É uma doença altamente contagiosa causada por variedade de bactérias aeróbias e anaeróbias. Diferentes antibióticos empregados no tratamento dessa doença têm apresentado elevada incidência de resistência bacteriana. Dentre os antibióticos de última geração, destaca-se o besifloxacino, antibiótico de quarta geração da classe das fluoroquinolonas, indicado exclusivamente para uso oftálmico tópico. Entretanto, esse fármaco possui baixa solubilidade em água, diminuindo sua biodisponibilidade. Tendo em vista superar esse desafio, foi proposta abordagem nanotecnológica para o desenvolvimento de nanocristais desse fármaco. A preparação de nanocristais de besifloxacino empregando moagem via úmida em escala reduzida foi promissora empregando tensoativo Povacoat®. O Diâmetro hidrodinâmico médio (DHM) da partícula foi de aproximadamente 550 nm, com índice de polidispersão (IP) menor que 0,2. Esse resultado permitiu aumentar a solubilidade de saturação em aproximadamente duas vezes em relação a matéria-prima, possibilitando aumentar a velocidade de dissolução desse fármaco e melhorar sua biodisponibilidade e segurança. Além disso, foi validado o método para quantificação do besifloxacino por CLAE, apresentando especificidade, linearidade no intervalo de 20 a 80µg/mL (r= 0,9996), precisão por repetibilidade (DPR= 1,20%, 0,84% e 0,39%), precisão intermediária (DPR= 0,94%) e exatidão 99,03%. Estudo de estabilidade acelerado (90 dias) na condição 40°C±2°C/75%UR±5%UR e estudo de estabilidade de acompanhamento (150 dias) na condição: 25°C ± 2°C / 60% UR ± 5% UR evidenciaram a estabilidade do teor no período avaliado. Ainda, a nanossuspensão de besifloxacino 0,6% m/m (nanocristais) na dose máxima (500 mg/kg) e o estabilizante Povacoat® (750 mg/kg) não apresentaram toxicidade em larvas de G. mellonella. A concentração inibitória mínima (CIM) para a formulação inovadora foi de 0,0960 µg/mL e 1,60 µg/mL frente a Staphylococcus aureus e Pseudomonas aeruginosa, respectivamente, confirmando eficácia in vitro

Bacterial conjunctivitis greatly impacts the population's health, presenting more than a third of eye diseases reported worldwide. It is an infection caused by various aerobic and anaerobic bacteria and is highly contagious. Therefore, it presents a high incidence of bacterial resistance to the antibiotics commonly used for treatment. Among the most recent antibiotics, besifloxacin is a fourth-generation fluoroquinolone antibiotic indicated exclusively for topical ophthalmic use. Due to its importance in treating bacterial conjunctivitis and its low solubility in the water, a nanotechnological approach was proposed to develop besifloxacin nanocrystals. The preparation of besifloxacin nanocrystals using small-scale wet milling was promising using Povacoat® surfactant. The particle's average hydrodynamic diameter (DHM) was approximately 550 nm, with a polydispersity index (IP) of less than 0.2. This result increased the saturation solubility approximately two times concerning the raw material, making it possible to increase the dissolution rate of this drug and improve its bioavailability and safety. In addition, the method for quantification of besifloxacin by HPLC was validated, presenting specificity, linearity in the range of 20 to 80µg/mL (r= 0.9996), precision by repeatability (DPR= 1.20%, 0.84% and 0.39%), intermediate precision (DPR= 0.94%) and accuracy 99.03%. Accelerated stability study (90 days) at 40°C±2°C/75%RH±5%RH condition and follow-up stability study (150 days) at 25°C ± 2°C / 60% RH ± condition 5% RH showed the stability of content in the evaluated period. Furthermore, the 0.6% besifloxacin nanosuspension (nanocrystals) at the maximum dose (500 mg/kg) and the Povacoat® stabilizer (750 mg/kg) did not show toxicity in G. mellonella larvae. The minimum inhibitory concentration (MIC) to innovative formulation was 0.0960 µg/mL and e 1.60 µg/mL against Staphylococcus aureus and Pseudomonas aeruginosa, respectively, confirming in vitro efficacy

Interaction study of Pasteurella multocida with culturable aerobic bacteria isolated from porcine respiratory tracts using coculture in conditioned media.

BACKGROUND: The porcine respiratory tract harbours multiple microorganisms, and the interactions between these organisms could be associated with animal health status. Pasteurella multocida is a culturable facultative anaerobic bacterium isolated from healthy and diseased porcine respiratory tracts. The interaction between P. multocida and other aerobic commensal bacteria in the porcine respiratory tract is not well understood. This study aimed to determine the interactions between porcine P. multocida capsular serotype A and D strains and other culturable aerobic bacteria isolated from porcine respiratory tracts using a coculture assay in conditioned media followed by calculation of the growth rates and interaction parameters. RESULTS: One hundred and sixteen bacterial samples were isolated from five porcine respiratory tracts, and 93 isolates were identified and phylogenetically classified into fourteen genera based on 16S rRNA sequences. Thirteen isolates from Gram-negative bacterial genera and two isolates from the Gram-positive bacterial genus were selected for coculture with P. multocida. From 17 × 17 (289) interaction pairs, the majority of 220 pairs had negative interactions indicating competition for nutrients and space, while 17 pairs were identified as mild cooperative or positive interactions indicating their coexistence. All conditioned media, except those of Acinetobacter, could inhibit P. multocida growth. Conversely, the conditioned media of P. multocida also inhibited the growth of nine isolates plus themselves. CONCLUSION: Negative interaction was the major interactions among the coculture of these 15 representative isolates and the coculture with P. multocida. The conditioned media in this study might be further analysed to identify critical molecules and examined by the in vivo experiments. The study proposed the possibility of using these molecules in conditioned media to control P. multocida growth.

Characteristics of aerobic vaginitis among women in Xi'an district: a hospital-based study.

BACKGROUND: Aerobic vaginitis (AV) is a reproductive tract infection that affects health of women. The objective of this study was to analyze the characteristics of simple and mixed AV patients in Xi'an district and provide reference data for the clinical treatment of AV. METHODS: Patients were recruited from the outpatient Department of Obstetrics and Gynecology in the First Affiliated Hospital of Xi'an Jiaotong University from September 2014 to April 2019 in strict accordance with inclusion and exclusion criteria. The study principally examined the vaginal ecosystem, age distribution, levels of functional enzymes, and changes in pH levels in these women. Differences within groups were analyzed. RESULTS: A total of 284 AV patients were enrolled to investigate the distribution of simple and mixed AV infection. AV infection was found to be mainly simple infection. Simple AV patients were generally aged 50-60 years, while mixed AV patients were mostly aged 30-40 years. In the present study, the density of vaginal bacteria (OR = 13.294, 95% CI = 5.869-30.115, P < 0.01), the type of predominant bacteria (OR = 3.962, 95% CI = 1.785-7.984, P < 0.01) and positive expression of coagulase (OR = 3.789, 95% CI = 1.798-7.984, P < 0.01) were considered risk factors for mixed AV infection. CONCLUSIONS: The epidemiology of simple and mixed AV infection were found to be different, with density of vaginal bacteria (I or IV), species that are predominant and levels of coagulase being risk factors for mixed AV infection.

Fecal cultivable aerobic microbiota of dairy cows and calves acting as reservoir of clinically relevant antimicrobial resistance genes.

Antimicrobial resistance has become a global threat to public health since multidrug-resistant (MDR) bacteria have been reported worldwide carrying different antimicrobial resistance genes (ARGs), and animals have been described as a reservoir of ARGs. The presence of antimicrobial-resistant bacteria and ARGs in the food matrix is a risk to public health. This study aimed to research the presence of clinically relevant ARGs for important antimicrobials and genetic elements in fecal samples from dairy cows and calves on a Brazilian farm. In this study, a total of 21 fecal samples were collected, and then, the DNA of cultivable aerobic bacteria was extracted. Fifty-seven ARGs and twenty-three genetic elements were researched by PCR and confirmed by sequencing. Several ARGs that confer resistance to ß-lactams, tetracyclines, fluoroquinolones, sulphonamides, phenicols, aminoglycoside, glycopeptides, and macrolides were detected. A total of 200 amplicons from 23 ARGs (blaCTX-M-Gp2, blaCMY, blaSHV, tetA, tetB, tetC, qepA, qnrB, qnrS, oqxA, oqxB, vanC1, vanC2/3, aadA, sul1, sul2, sul3, ermB, mefAE, floR, cmlA, aadA, aph(3')-Ia, aac(3')-Ia), and 145 amplicons from 12 genetic elements (IncF, IncFIA, IncFIB, IncI1, IncY, IncU, IncK, IncP, IncR, IncHI1, ColE-like, intI1) were detected. The results presented in this study call attention to the monitoring of antimicrobial resistance in dairy farms worldwide. MDR bacteria and ARGs can spread to different sources, including milk products, which are one of the most consumed products worldwide, representing a potential risk to human health.

[Aerobic bacteria from skin lesions in reptiles and their antimicrobial susceptibility]. / Aerobes Keimspektrum und Resistenzlage bei Hautläsionen von Reptilien.

OBJECTIVE: Bacterial skin infections are common in reptiles. Although many such infections are influenced by multifactorial problems, specific treatment of bacterial infections is an important consideration. The objective of this study was to evaluate the range of aerobic bacteria in skin lesions of reptiles and to determine their antimicrobial susceptibility. MATERIAL AND METHODS: Swabs of skin lesions from 219 reptiles were cultured for aerobic bacteria between January 2017 and June 2018. Isolates were identified based on growth on selective agar plates, biochemical parameters, as well as MALDI-TOF MS. Antibiotic susceptibility testing was carried out using the microdilution method. RESULTS: A total of 306 isolates were identified, mostly gram-negative, including Pseudomonas spp. (n = 48), Citrobacter spp. (n = 31, only in chelonians), aerobic spore-forming bacteria (n = 30), Aeromonas spp. (n = 20), Acinetobacter spp. (n = 20), Proteus spp. (n = 15), Staphylococcus spp. (n = 15), Klebsiella spp. (n = 13), Enterococcus spp. (n = 13), Morganella spp. (n = 11) as well as 78 other gram-negative and 12 other gram-positive bacteria. Colonization with 2 (n = 80) or more (n = 16) bacterial isolates was seen in 96 animals. Antibiotic susceptibility testing was carried out with 208 of the 306 isolated bacteria. Many isolates were sensitive (minimal inhibitory concentration [MIC] in µg/ml ≤ breakpoint) to enro- (E) and marbofloxacin (M): 86.4 % MIC ≤ 0.5 (E) and 95.5 % MIC ≤ 1 (M) for Pseudomonas spp., 86.4 % MIC ≤ 0.5 (E) and 90.9 % MIC ≤ 1 (M) for Citrobacter spp., 75.0 % MIC ≤ 0.5 (E) and 100 % MIC ≤ 1 (M) for Aeromonas spp. Trimethoprim/sulfamethoxazol proved to be effective against most of the Citrobacter spp. (90.9 % MIC ≤ 2/38) and Aeromonas spp. (75.0 % MIC ≤ 2/38). Amikacin was effective against nearly all Pseudomonas spp. (97.7 % MIC ≤ 16), Citrobacter spp. (95.5 % MIC ≤ 16) and Aeromonas spp. (93.8 % MIC ≤ 16). CONCLUSION AND CLINICAL RELEVANCE: The majority of isolates were gram-negative; the clinical relevance of individual isolates must, however, be evaluated on a case by case basis. Many of the isolated bacteria were sensitive to fluoroquinolones as well as aminoglycosides. Susceptibility testing is recommended since use of these antibiotics should be limited and for every tested group of antibiotics resistant isolates were found.

Composition of semen and foreskin mucosa aerobic microbiota and its impact on sperm parameters of captive collared peccaries (Pecari tajacu).

AIM: To evaluate the bacterial composition of collared peccary semen and foreskin mucosa, and to verify the sensitivity of isolates to antimicrobials used in semen conservation and to Aloe vera gel, which is an alternative external cryoprotectant. METHODS AND RESULTS: Nine foreskin mucosa and ejaculate samples from adult animals were used. Sperm characteristics and bacterial load were evaluated in fresh semen. The preputial mucosa and semen bacterial isolates were identified and tested against five concentrations of each antimicrobial (streptomycin-penicillin and gentamicin) and A. vera gel. Corynebacterium sp. and Staphylococcus sp. were isolated in greater numbers than others in both semen (64·10 and 20·51%, respectively) and the foreskin mucosa (60·60 and 24·25%, respectively), and ranged from 0·4 to 21 × 105 colony-forming units (CFU) per ml. The average load of Corynebacterium sp. was negatively correlated (P < 0·05) with the sperm membrane integrity (r = -0·73055) and curvilinear velocity (r = -0·69048). Streptomycin-penicillin and gentamicin inhibited most micro-organisms, and A. vera showed lower antimicrobial activity. CONCLUSION: Several Gram-positive bacteria are present in semen and foreskin mucosa of collared peccary, and the benefits of using primarily penicillin-streptomycin and gentamicin antimicrobials in the bacterial control of diluted semen of these animals are strongly indicated. SIGNIFICANCE AND IMPACT OF THE STUDY: This study provides insight into the reproductive microbiota of captive male-collared peccary. This work provides a theoretical basis to assist reproductive biotechnologies for ex situ conservation of the species.

Topical Oxygen Therapy Shifts Microbiome Dynamics in Chronic Diabetic Foot Ulcers.

INTRODUCTION: Bacterial biofilm in wounds prevents healing by acting as a physical barrier to wound closure and hyperactivating local inflammatory processes, thus making its removal a high priority. The authors previously have shown that adding topical oxygen to standard wound care increased healing of Texas Grade II and III diabetic foot ulcers (DFUs), which they hypothesized was a result of alterations of the wound microbiome/biofilm. OBJECTIVE: This study aims to determine the mechanism of action of topical oxygen in DFUs by examining the diversity of bacterial genera present in DFUs treated with topical oxygen. MATERIALS AND METHODS: Six patients with chronic DFUs had their wounds swabbed weekly over an 8-week period of continuous topical oxygen treatment, and microbiome diversity was assessed by metagenomic 16S rDNA sequencing using a next-generation sequencing platform. RESULTS: The wound microbiome shifted toward a diverse flora dominated by aerobes and facultative anaerobes with oxygen therapy in 5 healed wounds. In contrast, anaerobic flora persisted in a single nonhealing ulcer in the present study cohort. CONCLUSIONS: Although the sample size was small, this study suggests topical oxygen therapy may have the ability to encourage the growth of aerobic members of the wound microbiome and be an effective alternative to antibiotics in this area.

The prevalence of the culturable human skin aerobic bacteria in Riyadh, Saudi Arabia.

BACKGROUND: Human skin is an appropriate environment for the growth of different types of microbes that may inhabit the skin as commensal flora. This study aims at identifying the diversity of skin microbiota in healthy Saudi population. In this study, 80 Saudi subjects of both males and females, from different habitat, and different ages (elderly and young), were recruited to determine the aerobic bacterial flora from their three skin sites; hand, scalp and foot. A single colony obtained from aerobic culture was identified using Biomérieux VITEK® 2 system. For those not being identified by VITEK® 2 system, the identification was conducted using 16 s rRNA sequence. RESULTS: Thirty-three bacterial species were isolated from males, whilst 24 species were isolated from females. Micrococci are the predominant organisms, followed by Staphylococci, Pantoea species, and lastly Enterococcus faecium. Acinetobacter baumannii, Enterococcus faecalis, and Klebsiella pneumoniae were only found in elder subjects, while Pseudomonas aeruginosa was isolated from the young only. The number of bacterial isolates in the elders was higher that of the young. The average number of flora was larger in foot, then hand and lastly scalp. CONCLUSION: Here we show the difference in the number of cultivable bacteria across age and gender that may result in the variety of local skin infection. This study paves the way to further investigation in the aspect of in-depth metagenomics analysis and host-pathogen interaction.

Seasonal dynamics of aerobic anoxygenic phototrophs in freshwater lake Vlkov.

Aerobic anoxygenic phototrophic (AAP) bacteria are a common component of freshwater microbial communities. They harvest light energy using bacteriochlorophyll a-containing reaction centers to supplement their predominantly heterotrophic metabolism. We used epifluorescence microscopy, HPLC, and infrared fluorometry to examine the dynamics of AAP bacteria in the mesotrophic lake Vlkov during the seasonal cycle. The mortality of AAP bacteria was estimated from diel changes of bacteriochlorophyll a fluorescence. The AAP abundance correlated with water temperature and DOC concentration. Its maximum was registered during late summer, when AAP bacteria made up 20% of total bacteria. The novel element of this study is the seasonal measurements of AAP mortality rates. The rates ranged between 1.15 and 4.56 per day with the maxima registered in early summer coinciding with the peak of primary production, which documents that AAP bacteria are a highly active component of freshwater microbial loop.

Evaluation of cultivable aerobic bacterial flora from Russell's viper (Daboia russelii) oral cavity.

Snake mouths contain a wide range of bacteria. Identifying these bacteria in snakes is very important to obtain an understanding of the etiological agents of secondary infections that may result from accidents during handling and/or snake bites. The present study aims to determine the pattern of oral bacterial flora of nine healthy Russell's vipers (Daboia russelii), and their susceptibility to common antibiotics. A total of 94 isolates were obtained in pure form, which demonstrated noticeable colony characteristics and which were further studied with several biochemical tests. The strains that showed distinctive colonies, morphology and biochemical parameters were additionally subjected to phylogenetic characterization using 16S rRNA gene sequences. Furthermore, all these isolates were studied for antibiotic susceptibility. The oral cavity of the Russell's viper harbors a wide range of pathogenic bacteria, including Gram-negative genera: Proteus sp., Pseudomonas sp., Salmonella sp., Providencia sp., Alcaligenes sp., Morganella sp., as well as E. coli, and Gram-positive genera: Bacillus and Enterococcus sp., Staphylococcus sp. and Lysinobacillus sp. Most of the isolates were resistant to antibiotics viz. penicillin, Amoxyclav, oxacillin, methicillin and streptomycin while sensitive towards imipenem, amikacin, norfloxacin, gatifloxacin, ciprofloxacin, gentamicin, tetracycline, chloramphenicol and azithromycin. The present study documents diverse bacteria predominant in the oral cavity of Daboia russelii and studied their antibiotic susceptibilities.

Long-term seasonal and interannual variability of marine aerobic anoxygenic photoheterotrophic bacteria.

We studied the long-term temporal dynamics of the aerobic anoxygenic phototrophic (AAP) bacteria, a relevant functional group in the coastal marine microbial food web, using high-throughput sequencing of the pufM gene coupled with multivariate, time series and co-occurrence analyses at the Blanes Bay Microbial Observatory (NW Mediterranean). Additionally, using metagenomics, we tested whether the used primers captured accurately the seasonality of the most relevant AAP groups. Phylogroup K (Gammaproteobacteria) was the greatest contributor to community structure over all seasons, with phylogroups E and G (Alphaproteobacteria) being prevalent in spring. Diversity indices showed a clear seasonal trend, with maximum values in winter, which was inverse to that of AAP abundance. Multivariate analyses revealed sample clustering by season, with a relevant proportion of the variance explained by day length, temperature, salinity, phototrophic nanoflagellate abundance, chlorophyll a, and silicate concentration. Time series analysis showed robust rhythmic patterns of co-occurrence, but distinct seasonal behaviors within the same phylogroup, and even within different amplicon sequence variants (ASVs) conforming the same operational taxonomic unit (OTU). Altogether, our results picture the AAP assemblage as highly seasonal and recurrent but containing ecotypes showing distinctive temporal niche partitioning, rather than being a cohesive functional group.

Isolation and characterization of aerobic, culturable, arsenic-tolerant bacteria from lead-zinc mine tailing in southern China.

Bioremediation of arsenic (As) pollution is an important environmental issue. The present investigation was carried out to isolate As-resistant novel bacteria and characterize their As transformation and tolerance ability. A total of 170 As-resistant bacteria were isolated from As-contaminated soils at the Kangjiawan lead-zinc tailing mine, located in Hunan Province, southern China. Thirteen As-resistant isolates were screened by exposure to 260 mM Na2HAsO4·7H2O, most of which showed a very high level of resistance to As5+ (MIC ≥ 600 mM) and As3+ (MIC ≥ 10 mM). Sequence analysis of 16S rRNA genes indicated that the 13 isolates tested belong to the phyla Firmicutes, Proteobacteria and Actinobacteria, and these isolates were assigned to eight genera, Bacillus, Williamsia, Citricoccus, Rhodococcus, Arthrobacter, Ochrobactrum, Pseudomonas and Sphingomonas. Genes involved in As resistance were present in 11 of the isolates. All 13 strains transformed As (1 mM); the oxidation and reduction rates were 5-30% and 10-51.2% within 72 h, respectively. The rates of oxidation by Bacillus sp. Tw1 and Pseudomonas spp. Tw224 peaked at 42.48 and 34.94% at 120 h, respectively. For Pseudomonas spp. Tw224 and Bacillus sp. Tw133, the highest reduction rates were 52.01% at 48 h and 48.66% at 144 h, respectively. Our findings will facilitate further research into As metabolism and bioremediation of As pollution by genome sequencing and genes modification.

Non-halophilic endophytes associated with the euhalophyte Arthrocnemum macrostachyum and their plant growth promoting activity potential.

Numerous microbial taxa establish natural relations with plants, and especially endophytes can be relevant in the development and growth promotion of their host. In this work, we explore the diversity of non-halophilic microorganisms inhabiting the endosphere of the halophyte Arthrocnemum macrostachyum. A total of 1045 isolates were recovered using standard non-saline media, which clustered into 22 operational phylogenetic units (OPUs) including 7 putative new species and 13 OPUs not previously detected as endophytes. The more abundant isolates corresponded to close relatives of Kushneria indalinina/K. marisflavi, Providencia rettgeri, Pseudomonas zhaodongensis and Bacillus safensis, which made up to ∼ 62% of the total isolates. We also isolated OPUs not detected by the culture-independent approach reinforcing the need of culturing to reveal the microbial diversity associated with plants. Additionally, the plant growth promoting activity was evaluated by representative strains of the more abundant OPUs (total = 94 strains) including also some previously isolated halophiles from the same plants. Under both saline and non-saline conditions, some strains principally those affiliated to Paenibacillus borealis, Staphylococcus equorum, Salinicola halophilus and Marinococcus tarijensis, presented growth promoting activity in Arabidopsis thaliana, which was evaluated as an increment of weight and root length.

Aerobic microbial taxa dominate deep subsurface cores from the Alberta oil sands.

Little is known about the microbial ecology of the subsurface oil sands in Northern Alberta, Canada. Biodegradation of low molecular weight hydrocarbons by indigenous microbes has enriched high molecular weight hydrocarbons, resulting in highly viscous bitumen. This extreme subsurface environment is further characterized by low nutrient availability and limited access to water, thus resulting in low microbial biomass. Improved DNA isolation protocols and increasingly sensitive sequencing methods have allowed an in-depth investigation of the microbial ecology of this unique subsurface environmental niche. Community analysis was performed on core samples (n = 62) that were retrieved from two adjacent sites located in the Athabasca Oil Sands at depths from 220 to 320 m below the surface. Microbial communities were dominated by aerobic taxa, including Pseudomonas and Acinetobacter. Only one core sample microbial community was dominated by anaerobic taxa, including the methanogen Methanoculleus, as well as Desulfomicrobium and Thauera. Although the temperature of the bitumen-containing subsurface is low (8°C), two core samples had high fractions of the potentially thermophilic taxon, Thermus. Predominance of aerobic taxa in the subsurface suggests the potential for in situ aerobic hydrocarbon degradation; however, more studies are required to determine the functional role of these taxa within this unique environment.

Taxonomically-linked growth phenotypes during arsenic stress among arsenic resistant bacteria isolated from soils overlying the Centralia coal seam fire.

Arsenic (As), a toxic element, has impacted life since early Earth. Thus, microorganisms have evolved many As resistance and tolerance mechanisms to improve their survival outcomes given As exposure. We isolated As resistant bacteria from Centralia, PA, the site of an underground coal seam fire that has been burning since 1962. From a 57.4°C soil collected from a vent above the fire, we isolated 25 unique aerobic As resistant bacterial strains spanning seven genera. We examined their diversity, resistance gene content, transformation abilities, inhibitory concentrations, and growth phenotypes. Although As concentrations were low at the time of soil collection (2.58 ppm), isolates had high minimum inhibitory concentrations (MICs) of arsenate and arsenite (>300 mM and 20 mM respectively), and most isolates were capable of arsenate reduction. We screened isolates (PCR and sequencing) using 12 published primer sets for six As resistance genes (AsRGs). Genes encoding arsenate reductase (arsC) and arsenite efflux pumps (arsB, ACR3(2)) were present, and phylogenetic incongruence between 16S rRNA genes and AsRGs provided evidence for horizontal gene transfer. A detailed investigation of differences in isolate growth phenotypes across As concentrations (lag time to exponential growth, maximum growth rate, and maximum OD590) showed a relationship with taxonomy, providing information that could help to predict an isolate's performance given As exposure in situ. Our results suggest that microbiological management and remediation of environmental As could be informed by taxonomically-linked As tolerance, potential for resistance gene transferability, and the rare biosphere.

Phylogeny and genomics of SAUL, an enigmatic bacterial lineage frequently associated with marine sponges.

Many marine sponges contain dense and diverse communities of associated microorganisms. Members of the 'sponge-associated unclassified lineage' (SAUL) are frequently recorded from sponges, yet little is known about these bacteria. Here we investigated the distribution and phylogenetic status of SAUL. A meta-analysis of the available literature revealed the widespread distribution of this clade and its association with taxonomically varied sponge hosts. Phylogenetic analyses, conducted using both 16S rRNA gene-based phylogeny and concatenated marker protein sequences, revealed that SAUL is a sister clade of the candidate phylum 'Latescibacteria'. Furthermore, we conducted a comprehensive analysis of two draft genomes assembled from sponge metagenomes, revealing novel insights into the physiology of this symbiont. Metabolic reconstruction suggested that SAUL members are aerobic bacteria with facultative anaerobic metabolism, with the capacity to degrade multiple sponge- and algae-derived carbohydrates. We described for the first time in a sponge symbiont the putative genomic capacity to transport phosphate into the cell and to produce and store polyphosphate granules, presumably constituting a phosphate reservoir for the sponge host in deprivation periods. Our findings suggest that the lifestyle of SAUL is symbiotic with the host sponge, and identify symbiont factors which may facilitate the establishment and maintenance of this relationship.

Longitudinal Analyses of Gut-Associated Bacterial Microbiota in Ulcerative Colitis Patients.

BACKGROUND: The normal colonic microbiota is associated with the etiology of ulcerative colitis (UC). Several bacterial species are associated with the initiation and amplification of disease process. However, the etiology and mechanism of UC are poorly understood. The present study aimed to investigate, characterize, and compare the main composition of the mucosa-associated intestinal microflora in colonoscopic biopsy specimens of UC and non-UC patients. METHODS: Aerobic and facultative-anaerobic mucosa-associated bacteria were isolated and diagnosed from colonoscopic biopsy specimens of 40 UC patients and 40 patients without UC. Patients were selected as control from the same centers and colonoscopy was carried out for other reasons (mainly colorectal screening). Isolation and characterization for aerobic and facultative-anaerobic intestinal bacteria were carried out by conventional culture techniques. DNA extraction from biopsies and polymerase chain reaction (PCR) amplification of bacterial 16S rRNA with gene-targeted and species-specific primers was performed for detection of anaerobic bacterial species. RESULTS: Several species of mucosa-associated aerobic and facultative anaerobic bacteria were found in biopsy specimens and there were no significant differences between UC patients and non-UC patients. Our investigation for detection of the anaerobic intestinal flora showed Faecalibacterium prausnitzii, Prevotella, and Peptostreptococcus productus were the predominant microflora in controls and have significant differences (P = 0.002, 0.025 and 0.039, respectively). CONCLUSION: This is the first investigation of the intestinal mucosa-associated microflora in patients with UC in Iran. These results, although limited by sample size, allow a better understanding of changes in mucosa-associated bacterial flora in these patients, showing that decrease of Faecalibacterium prausnitzii, Provetella, and Peptostreptococcus productus in the intestinal tract may translate into a reduction in the important role of this beneficial bacterial species, which can lead to reduced protection of the gut mucosa and UC development.

Isolation and identification of an aerobic denitrifying phosphorus removing bacteria and analysis of the factors influencing denitrification and phosphorus removal.

Excessive emission of plant nutrients (such as nitrogen and phosphorus) into the water body can induce eutrophication. Therefore, how to control eutrophic water efficiently and economically is very important. In the paper, highly efficient aerobic denitrifying phosphorus removing J16 bacteria was isolated from the activated sludge of an aerobic bioreactor in Taiyuan municipal wastewater treatment plant by using the blue-white spot screening method, an aerobic phosphorus absorption test, nitrate reduction test, nitrogen removal experiments, and plate coating and streaking methods. Through 16S rDNA gene homology comparison and physiological and biochemical identification, the J16 strain was preliminarily identified as Escherichia coli, with a sequence similarity of 99%. The 16S rDNA sequence of strain J16 was submitted to GenBank (accession number: MF667015). The effect of temperature, pH, percentage of inoculum and phosphate-P (PO4 3--P) concentration on denitrification and phosphorus removal efficiency was investigated through a single-factor experiment. The optimum conditions of the J16 strain for denitrification and phosphorus removal were as follows: 30°C, neutral or weak alkaline (pH: 7.2-8), and 3% of inoculum, respectively. The denitrification and phosphorus removal efficiency of strain J16 was the highest when PO4 3--P and nitrate-N(NO3 --N) concentrations were 8.9 and 69.31 mg/L, and the removal were 96.03% and 94.55%, respectively. In addition, strain J16 could reduce phosphoric acid to phosphine (PH3) and remove some phosphorus under hypoxia conditions. This is the first study to report the involvement of Escherichia coli in nitrogen and phosphorus removal under aerobic and hypoxia conditions. Based on the above results, the strain J16 can effectively remove nitrogen and phosphorus, and will be utilized in enhancing treatment of nitrogen and phosphorus-containing industrial wastewater and phosphorus reclamation.