Using PacBio sequencing to investigate the effects of treatment with lactic acid bacteria or antibiotics on cow endometritis

BACKGROUND: Endometritis is the most common disease of dairy cows and traditionally treated with antibiotics. Lactic acid bacteria can inhibit the growth of pathogens and also have potential for treatment of endometritis. Using PacBio single-molecule real-time sequencing technology, we sequenced the fulllength l6S rRNA of the microbiota in uterine mucus samples from 31 cows with endometritis, treated with lactic acid bacteria (experimental [E] group) and antibiotics (control [C] group) separately. Microbiota profiles taken before and after treatment were compared. RESULTS: After both treatments, bacterial species richness was significantly higher than before, but there was no significant difference in bacterial diversity. Abundance of some bacteria increased after both lactic acid bacteria and antibiotic treatment: Lactobacillus helveticus, Lactococcus lactis, Lactococcus raffinolactis, Pseudomonas alcaligenes and Pseudomonas veronii. The bacterial species that significantly decreased in abundance varied depending on whether the cows had been treated with lactic acid bacteria or antibiotics. Abundance of Staphylococcus equorum and Treponema brennaborense increased after lactic acid bacteria treatment but decreased after antibiotic treatment. According to COG-based functional metagenomic predictions, 384 functional proteins were significantly differently expressed after treatment. E and C group protein expression pathways were significantly higher than before treatment (p < 0.05). CONCLUSIONS: In this study, we found that lactic acid bacteria could cure endometritis and restore a normal physiological state, while avoiding the disadvantages of antibiotic treatment, such as the reductions in abundance of beneficial microbiota. This suggests that lactic acid bacteria treatment has potential as an alternative to antibiotics in the treatment of endometritis in cattle.

Correlación entre los microorganismos oxidantes del amonio y los factores ambientales durante el compostaje de estiércol de ganado / Correlation between ammonia-oxidizing microorganisms and environmental factors during cattle manure composting

Abstract Cattle manure composting was performed in an aerated vessel. Community structure and diversity of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) were investigated using polymerase chain reaction and denaturing gradient gel electrophoresis (PCR-DGGE) techniques targeting the ammonia monooxygenase alpha subunit (amoA) gene and the correlation between AOB and AOA communities and environmental factors was explored. Thirteen (13) AOB sequences were obtained, which were closely related to Nitrosomonas spp., Nitrosomonas eutropha, and Nitrosospira spp. and uncultured bacteria, among which Nitrosomonas spp. were predominant. Excessively high temperature and high ammonium concentration were not favorable for AOB growth. Five AOA sequences, belonging to Candidatus Nitrososphaera gargensis and to an uncultured archaeon, were obtained. During composting, community diversity of AOB and AOA fluctuated, with AOA showing a higher Shannon-Wiener index. The AOB community changed more dramatically in the mesophilic stage and the early thermophilic stage, whereas the most obvious AOA community succession occurred in the late thermophilic stage, the cooling stage and the maturity stage. Water content, total nitrogen (TN) and ammonium concentration were more relevant to the AOB community structure, while higher correlations were observed between ammonia, nitrate and TN and the AOA community. AOB community diversity was negatively correlated with pH (r = -0.938, p < 0.01) and water content (r = -0.765, p < 0.05), while positively correlated with TN (r = 0.894, p < 0.01). AOA community diversity was negatively correlated with ammonium concentration (r = -0.901, p < 0.01). Ammonium concentration played an important role in the succession of AOB and AOA communities during composting.

Resumen Se llevó a cabo un compostaje de estiércol de ganado en un recipiente aireado. Se investigó la estructura de la comunidad y la diversidad de bacterias oxidantes del amoníaco (AOB) y las arqueas oxidantes del amoníaco (AOA) mediante el uso de las técnicas de reacción en cadena de la polimerasa y la electroforesis en gel con gradiente de desnaturalización (PCR-DGGE) dirigidas al gen de la subunidad alfa de la amonio monooxigenasa (amoA), y se exploró la correlación entre las comunidades AOB, AOA y los factores ambientales. Se obtuvieron 13 secuencias de AOB, las cuales se relacionaron estrechamente con Nitrosomonas spp., Nitrosomonas eutropha y Nitrosospira spp., y bacterias no cultivadas, entre las cuales fueron predominantes las Nitrosomonas spp. La temperatura excesivamente alta y la concentración de amonio elevada no fueron favorables para el crecimiento de las AOB. Se obtuvieron 5 secuencias de AOA, pertenecientes a Candidatus Nitrososphaera gargensis y un Archaeon no cultivado. Durante el compostaje, la diversidad de AOB y AOA fluctuó y las AOA mostraron un índice de Shannon-Wiener más alto. La comunidad de AOB cambió significativamente en la etapa mesofílica y la etapa termofílica temprana, mientras que la sucesión más obvia de la comunidad AOA ocurrió en la etapa termofílica tardía y las etapas de enfriamiento y de maduración. El contenido de agua, el nitrógeno total (TN) y la concentración de amonio fueron más relevantes para la estructura de la comunidad AOB, mientras que se observaron correlaciones mayores entre amoníaco, nitrato y TN, y la comunidad AOA. La diversidad de la comunidad AOB se correlacionó negativamente con el pH (r= -0,938; p < 0,01) y el contenido de agua (r = -0,765; p < 0,05), mientras que se relacionó positivamente con TN (r = 0,894; p < 0,01). La diversidad de la comunidad AOA se correlacionó negativamente con la concentración de amonio (r = -0,901; p < 0,01). La concentración de amonio desempenó un papel importante en la sucesión de las comunidades AOB y AOA durante el compostaje.

Diversidad bacteriana en el biocátodo reductor de Cr(VI) de una Celda de Combustible Microbiana con puente salino / Bacterial diversity in the Cr(VI) reducing biocathode of a Microbial Fuel Cell with salt bridge

Although Cr(VI)-reducing and/or tolerant microorganisms have been investigated, there is no detailed information on the composition of the microbial community of the biocathode microbial fuel cell for Cr(VI) reduction. In this investigation, the bacterial diversity of a biocathode was analyzed using 454 pyrosequencing of the 16S rRNA gene. It was found that most bacteria belonged to phylum Proteobacteria (78.8%), Firmicutes (7.9%), Actinobacteria (6.6%) and Bacteroidetes (5.5%), commonly present in environments contaminated with Cr(VI). The dominance of the genus Pseudomonas (34.87%), followed by the genera Stenotrophomonas (5.8%), Shinella (4%), Papillibacter (3.96%), Brevundimonas (3.91%), Pseu-dochrobactrum (3.54%), Ochrobactrum (3.49%), Hydrogenophaga (2.88%), Rhodococcus (2.88%), Fluviicola (2.35%), and Alcaligenes (2.3%), was found. It is emphasized that some genera have not previously been associated with Cr(VI) reduction. This biocathode from waters contaminated with tannery effluents was able to remove Cr(VI) (97.83%) in the cathodic chamber. Additionally, through use of anaerobic sludge in the anodic chamber, the removal of 76.6% of organic matter (glucose) from synthetic waste water was achieved. In this study, an efficient biocathode for the reduction of Cr(VI) with future use in bioremediation, was characterized.

Aunque se ha investigado sobre los microorganismos reductores y/o tolerantes de Cr(VI), no hay información detallada sobre la composición de la comunidad microbiana del cátodo de una Celda de Combustible Microbiana para la reducción de Cr(VI). En esta investigación se analizó la diversidad bacteriana de un biocátodo usando pirosecuenciación 454 del gen 16S rRNA. Se encontró que la mayoría de las bacterias pertenecieron a los filos Proteobac-teria (78,8%), Firmicutes (7,9%), Actinobacteria (6,6%) y Bacteroidetes (5,5%), comúnmente presentes en ambientes contaminados con Cr(VI). Se encontró como género dominante a Pseudomonas (34,87%), seguido por los géneros Stenotrophomonas (5,8%), Shinella (4%), Papil-libacter (3,96%), Brevundimonas (3,91%), Pseudochrobactrum (3,54%), Ochrobactrum (3,49%), Hydrogenophaga (2,88%), Rhodococcus (2,88%), Fluviicola (2,35%) y Alcaligenes (2,3%). Se destaca que algunos géneros no han sido previamente asociados con la reducción de Cr(VI). Este biocátodo procedente de aguas contaminadas con efluentes de curtiembres fue capaz de remover Cr(VI) (97,83%) en la cámara catódica. Adicionalmente, a través del uso de lodo anaeróbico en la cámara anódica, se logró la remoción del 76,6% de materia orgánica (glucosa) a partir de agua residual sintética. En este estudio se caracterizó un eficiente biocátodo para la reducción de Cr(VI) con futuro uso en biorremediación.

Identification of bacterial and fungal species in human cadavers used in anatomy teaching / Identificación de especies bacterianas y fúngicas en cadáveres humanos utilizados en la enseñanza de la anatomía

Within the framework of undergraduate and postgraduate medical education, cadavers have been used to teach anatomy by dissection or by using prosected specimens. To accomplish this, an appropriated preservation process must guarantee that the cadaver is kept safe for harm, destruction, and decomposition. Embalming fluid contains fixatives, disinfectants, surfactants, buffers, salt, and water, making the cadaver safe for teaching anatomy. However, it remains unclear if there is any risk of dissemination of microorganisms during anatomy teaching, research, and dissection procedures on fixed cadavers. The purpose of this study is to identify bacterial and fungal species in fixed cadaveric material used in anatomy teaching. Samples of cadavers and anatomical sections were cultured and biochemical tests and molecular identification by polymerase chain reaction (PCR) were performed to identify the microorganisms. The results indicate that fixed cadaveric material has viable bacteria on its surfaces and almost all these correspond to gram-negative bacilli of the Enterobacteriaceae family. In conclusion, fixed cadavers could be a reservoir of bacteria. This study underscores the importance of generating safe manipulation protocols to avoid eventual contamination and disease.

Dentro del curriculum de los programas de postgrado y pregrado de las carreras de la salud, los cadáveres han sido utilizados para la enseñanza de la anatomía mediante la disección o utilizando preparados anatómicos. Para poder llevar a cabo esto, el cadáver debe pasar por un adecuado proceso de preservación; en el que se utilizan fluidos que contienen fijadores, desinfectantes, surfactantes, buffers, sal y agua, los cuales lo protegen del deterioro y la descomposición. Las soluciones fijadoras y conservadoras contienen desinfectantes, surfactantes, fijadores, buffers, sal y agua, que hacen que el cadáver sea seguro para la enseñanza de la anatomía. Sin embargo, no está claro si existe algún riesgo de diseminación de microorganismos durante la enseñanza, investigación y/o disección en estos cadáveres. El propósito del estudio es identificar especies bacterianas y/o fúngicas en material cadavérico previamente fijado, usado en la enseñanza de la anatomía. Se realizaron cultivos y técnicas de identificación molecular mediante reacción en cadena de polimerasa de muestras tomadas desde material cadavérico para identificar los microorganismos encontrados. Los resultados indican que el material cadavérico previamente fijado posee bacterias en sus superficies, la mayoría corresponde a bacilos gram negativos de la familia de las Enterobacteriaceae. En conclusión, los cadáveres previamente fijados pueden ser reservorio de bacterias. Este estudio destaca la importancia de generar protocolos de manipulación con el fin de evitar una posible contaminación y enfermedad.

Cultivated bacterial diversity associated with the carnivorous plant Utricularia breviscapa (Lentibulariaceae) from floodplains in Brazil

ABSTRACT Carnivorous plant species, such as Utricularia spp., capture and digest prey. This digestion can occur through the secretion of plant digestive enzymes and/or by bacterial digestive enzymes. To comprehend the physiological mechanisms of carnivorous plants, it is essential to understand the microbial diversity related to these plants. Therefore, in the present study, we isolated and classified bacteria from different organs of Utricularia breviscapa (stolons and utricles) and from different geographic locations (São Paulo and Mato Grosso). We were able to build the first bacterium collection for U. breviscapa and study the diversity of cultivable bacteria. The results show that U. breviscapa bacterial diversity varied according to the geographic isolation site (São Paulo and Mato Grosso) but not the analyzed organs (utricle and stolon). We reported that six genera were common to both sample sites (São Paulo and Mato Grosso). These genera have previously been reported to be beneficial to plants, as well as related to the bioremediation process, showing that these isolates present great biotechnological and agricultural potential. This is the first report of an Acidobacteria isolated from U. breviscapa. The role of these bacteria inside the plant must be further investigated in order to understand their population dynamics within the host.

Variations in culturable bacterial communities and biochemical properties in the foreland of the retreating Tianshan No. 1 glacier

Abstract As a glacier retreats, barren areas are exposed, and these barren areas are ideal sites to study microbial succession. In this study, we characterized the soil culturable bacterial communities and biochemical parameters of early successional soils from a receding glacier in the Tianshan Mountains. The total number of culturable bacteria ranged from 2.19 × 105 to 1.30 × 106 CFU g-1 dw and from 9.33 × 105 to 2.53 × 106 CFU g-1 dw at 4 °C and 25 °C, respectively. The number of culturable bacteria in the soil increased at 25 °C but decreased at 4 °C along the chronosequence. The total organic carbon, total nitrogen content, and enzymatic activity were relatively low in the glacier foreland. The number of culturable bacteria isolated at 25 °C was significantly positively correlated with the TOC and TN as well as the soil urease, protease, polyphenoloxidase, sucrase, catalase, and dehydrogenase activities. We obtained 358 isolates from the glacier foreland soils that clustered into 35 groups using amplified ribosomal DNA restriction analysis. These groups are affiliated with 20 genera that belong to six taxa, namely, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Actinobacteria, Bacteroides, and Deinococcus-Thermus, with a predominance of members of Actinobacteria and Proteobacteria in all of the samples. A redundancy analysis showed that the bacterial succession was divided into three periods, an early stage (10a), a middle stage (25-74a), and a late stage (100-130a), with the total number of culturable bacteria mainly being affected by the soil enzymatic activity, suggesting that the microbial succession correlated with the soil age along the foreland.

Changes in antimicrobial susceptibility of commonly clinically significant isolates before and after the interventions on surgical prophylactic antibiotics (SPAs) in Shanghai

Abstract Surveillances and interventions on antibiotics use have been suggested to improve serious drug-resistance worldwide. Since 2007, our hospital have proposed many measures for regulating surgical prophylactic antibiotics (carbapenems, third gen. cephalosporins, vancomycin, etc.) prescribing practices, like formulary restriction or replacement for surgical prophylactic antibiotics and timely feedback. To assess the impacts on drug-resistance after interventions, we enrolled infected patients in 2006 (pre-intervention period) and 2014 (post-intervention period) in a tertiary hospital in Shanghai. Proportions of targeted pathogens were analyzed: methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococcus spp. (VRE), imipenem-resistant Escherichia coli (IREC), imipenem-resistant Klebsiella pneumoniae (IRKP), imipenem-resistant Acinetobacter baumannii (IRAB) and imipenem-resistant Pseudomonas aeruginosa (IRPA) isolates. Rates of them were estimated and compared between Surgical Department, ICU and Internal Department during two periods. The total proportions of targeted isolates in Surgical Department (62.44%, 2006; 64.09%, 2014) were more than those in ICU (46.13%, 2006; 50.99%, 2014) and in Internal Department (44.54%, 2006; 51.20%, 2014). Only MRSA has decreased significantly (80.48%, 2006; 55.97%, 2014) (p < 0.0001). The percentages of VRE and IREC in 3 departments were all <15%, and the slightest change were also both observed in Surgical Department (VRE: 0.76%, 2006; 2.03%, 2014) (IREC: 2.69%, 2006; 2.63%, 2014). The interventions on surgical prophylactic antibiotics can be effective for improving resistance; antimicrobial stewardship must be combined with infection control practices.

Trichoderma harzianum MTCC 5179 impacts the population and functional dynamics of microbial community in the rhizosphere of black pepper (Piper nigrum L )

Abstract Employing Illumina Hiseq whole genome metagenome sequencing approach, we studied the impact of Trichoderma harzianum on altering the microbial community and its functional dynamics in the rhizhosphere soil of black pepper (Piper nigrum L.). The metagenomic datasets from the rhizosphere with (treatment) and without (control) T. harzianum inoculation were annotated using dual approach, i.e., stand alone and MG-RAST. The probiotic application of T. harzianum in the rhizhosphere soil of black pepper impacted the population dynamics of rhizosphere bacteria, archae, eukaryote as reflected through the selective recruitment of bacteria [Acidobacteriaceae bacterium (p = 1.24e-12), Candidatus koribacter versatilis (p = 2.66e-10)] and fungi [(Fusarium oxysporum (p = 0.013), Talaromyces stipitatus (p = 0.219) and Pestalotiopsis fici (p = 0.443)] in terms of abundance in population and bacterial chemotaxis (p = 0.012), iron metabolism (p = 2.97e-5) with the reduction in abundance for pathogenicity islands (p = 7.30e-3), phages and prophages (p = 7.30e-3) with regard to functional abundance. Interestingly, it was found that the enriched functional metagenomic signatures on phytoremediation such as benzoate transport and degradation (p = 2.34e-4), and degradation of heterocyclic aromatic compounds (p = 3.59e-13) in the treatment influenced the rhizosphere micro ecosystem favoring growth and health of pepper plant. The population dynamics and functional richness of rhizosphere ecosystem in black pepper influenced by the treatment with T. harzianum provides the ecological importance of T. harzianum in the cultivation of black pepper.

Purification, characterization, mode of action, and enhanced production of Salivaricin mmaye1, a novel bacteriocin from Lactobacillus salivarius SPW1 of human gut origin

Background: Emergence of antibiotic resistance among pathogenic and food spoilage bacteria such as Staphylococcus aureus, Micrococcus luteus, Streptococcus pyogenes, Streptococcus sanguinis, Streptococcus mutans, Bacillus cereus, and Listeria monocytogenes triggered the search for alternative antimicrobials. An investigation aimed at purifying, characterizing, elucidating the mode of action, and enhancing the production of salivaricin from Lactobacillus salivarius of human gut origin was conducted. Results: Salivaricin mmaye1 is a novel bacteriocin purified from L. salivarius isolated from human feces. It is potent at micromolar concentrations and has a molecular weight of 1221.074 Da as determined by MALDI-TOF mass spectrometry. It has a broad spectrum of antibacterial activity. Salivaricin mmaye1 showed high thermal and chemical stability and moderate pH stability. The proteinaceous nature of salivaricin mmaye1 was revealed by the complete loss of activity after treatment with pepsin, trypsin, α-chymotrypsin, protease, and proteinase. Salivaricin mmaye1 is cell wall associated, and adsorption­desorption of the bacteriocin from the cell wall of the producer by pH modification proved successful. It exhibited a bactericidal mode of action mediated by pore formation. Its biosynthesis is regulated by a quorum sensing mechanism. Enhanced production of salivaricin mmaye1 was achieved in a newly developed growth medium. Conclusions: A novel, cell wall adhering, highly potent bacteriocin with a broad spectrum of inhibitory activity, membrane-permeabilizing ability, and enhanced production in a newly constituted medium has been isolated. It has a quorum sensing regulatory system and possesses interesting physicochemical characteristics favoring its future use in food biopreservation. These findings pave the way for future evaluation of its medical and food applications.

Análise da microbiota em tonômetros de aplanação de Goldmann / Analysis of the microbiota in Goldmann applanation tonometers

RESUMO Objetivos: Analisar a prevalência da microbiota nos tonômetros de aplanação de Goldmann nos consultórios do SUS e definir o grau de contaminação dos tonômetros e a eficácia da assepsia do cone do tonômetro de aplanação. Métodos: Estudo transversal em que foi realizado a coleta de 60 "swabs", divididos nos três tonômetros de aplanação dos ambulatórios do SUS em dois momentos distintos. No primeiro realizou-se a coleta no início dos atendimentos e no segundo momento, a coleta foi realizada ao final de todos os atendimentos. Todos "swabs" foram colhidos no meio Stuart e foi realizada a cultura em meio de bactérias. Resultados: Das 60 amostras, apenas uma apresentou crescimento de agente patogênico, a Escherichia coli. Conclusão: Independente dos vários métodos que o oftalmologista escolher para realizar a assepsia, a mesma é imprescindível para a manutenção de uma boa saúde ocular do paciente, evitando assim a transmissão e propagação de patógenos por meio do exame oftalmológico e concluímos também que o método utilizado pelo nosso serviço parece ser eficaz nesta profilaxia.

ABSTRACT Objective: Analyze the microbiota prevalence in the Goldmann applanation tonometers in the clinic of the SUS to define the contamination of the tonometers and the efficacy of asepsis of the applanation tonometer cone. Methods: A cross-sectional study was carried out to collect 60 "swabs" divided into the three aplanation tonometers of SUS clinics at two different times. In the first one, the collection will be performed at the beginning of the visits and at the second moment, the collection will be performed at the end of all the visits. All swabs will be harvested in the Stuart medium and culture was carried to sow bacteria. Results: Of the 60 samples, only one showed pathogen growth, Escherichia coli. Conclusion: Regardless of the various ways the ophthalmologist chooses to perform asepsis, it is essential for the maintenance of good patient eye health, thus avoiding the transmission and propagation of pathogens through ophthalmologic examination, and we also conclude that the method used by our patient seems to be effective in this prophylaxis.

Analysis of bacterial communities and characterization of antimicrobial strains from cave microbiota

Abstract In this study for the first-time microbial communities in the caves located in the mountain range of Hindu Kush were evaluated. The samples were analyzed using culture-independent (16S rRNA gene amplicon sequencing) and culture-dependent methods. The amplicon sequencing results revealed a broad taxonomic diversity, including 21 phyla and 20 candidate phyla. Proteobacteria were dominant in both caves, followed by Bacteroidetes, Actinobacteria, Firmicutes, Verrucomicrobia, Planctomycetes, and the archaeal phylum Euryarchaeota. Representative operational taxonomic units from Koat Maqbari Ghaar and Smasse-Rawo Ghaar were grouped into 235 and 445 different genera, respectively. Comparative analysis of the cultured bacterial isolates revealed distinct bacterial taxonomic profiles in the studied caves dominated by Proteobacteria in Koat Maqbari Ghaar and Firmicutes in Smasse-Rawo Ghaar. Majority of those isolates were associated with the genera Pseudomonas and Bacillus. Thirty strains among the identified isolates from both caves showed antimicrobial activity. Overall, the present study gave insight into the great bacterial taxonomic diversity and antimicrobial potential of the isolates from the previously uncharacterized caves located in the world's highest mountains range in the Indian sub-continent.

A thermophilic microorganism from Deception Island, Antarctica with a thermostable glutamate dehydrogenase activity

BACKGROUND: The Antarctic continent is a source of extreme microorganisms. Millions of years of isolation have produced unique biodiversity with adaptive responses to its extreme environment. Although the Antarctic climate is mainly cold, the presence of several geothermal sites, including thermal springs, fumaroles, hot soils and hydrothermal vents, provides ideal environments for the development of thermophilic and hyperthermophilic microorganisms. Their enzymes, called thermoenzymes, are the focus of interest in both academic and industrial research, mainly due to their high thermal activity and stability. Glutamate dehydrogenase, is an enzyme that plays a key role in the metabolism of carbon and nitrogen catalyzing reversibly the oxidative deamination of glutamate to alpha-ketoglutarate and ammonium. It belongs to the family of oxidoreductases, is widely distributed and it has been highly regarded for use as biosensors, particularly for their specificity and ability to operate in photochemical and electrochemical systems. However, the use of enzymes as biosensors is relatively problematic due to their instability to high temperatures, organic solvents and denaturing agents. The purpose of this study is to present the partial characterization of a thermophilic microorganism isolated from Deception Island, Antarctica, that displays glutamate dehydrogenase activity. RESULTS: In this work, we report the isolation of a thermophilic microorganism called PID15 from samples of Deception Island collected during the Antarctic Scientific Expedition ECA 46. This microorganism is a thermophile that grows optimally at 50 °C and pH 8.0. Scanning electron microscopy shows rod cells of 2.0 to 8.0 µm of length. Phylogenetic analysis of 16S rRNA gene revealed that this microorganism is closely related to Bacillus gelatini. This microorganism contains a thermostable glutamate dehydrogenase with optimal activity at pH 8.0 and temperatures for its activity from 37 to 50 °C, range of temperature of interest for biotechnological applications. This glutamate dehydrogenase is a highly thermostable enzyme. CONCLUSION: This is the first report of a microorganism from Antarctica containing a thermostable glutamate dehydrogenase that maintains its activity in a broad range of temperatures making it of potential interest for biotechnological applications.

Two mechanisms of oral malodor inhibition by zinc ions

Abstract Objectives The aim of this study was to reveal the mechanisms by which zinc ions inhibit oral malodor. Material and Methods The direct binding of zinc ions to gaseous hydrogen sulfide (H2S) was assessed in comparison with other metal ions. Nine metal chlorides and six metal acetates were examined. To understand the strength of H2S volatilization inhibition, the minimum concentration needed to inhibit H2S volatilization was determined using serial dilution methods. Subsequently, the inhibitory activities of zinc ions on the growth of six oral bacterial strains related to volatile sulfur compound (VSC) production and three strains not related to VSC production were evaluated. Results Aqueous solutions of ZnCl2, CdCl2, CuCl2, (CH3COO)2Zn, (CH3COO)2Cd, (CH3COO)2Cu, and CH3COOAg inhibited H2S volatilization almost entirely. The strengths of H2S volatilization inhibition were in the order Ag+ > Cd2+ > Cu2+ > Zn2+. The effect of zinc ions on the growth of oral bacteria was strain-dependent. Fusobacterium nucleatum ATCC 25586 was the most sensitive, as it was suppressed by medium containing 0.001% zinc ions. Conclusions Zinc ions have an inhibitory effect on oral malodor involving the two mechanisms of direct binding with gaseous H2S and suppressing the growth of VSC-producing oral bacteria.

Disruption of the Gut Ecosystem by Antibiotics

The intestinal microbiota is a complex ecosystem consisting of various microorganisms that expands human genetic repertoire and therefore affects human health and disease. The metabolic processes and signal transduction pathways of the host and intestinal microorganisms are intimately linked, and abnormal progression of each process leads to changes in the intestinal environment. Alterations in microbial communities lead to changes in functional structures based on the metabolites produced in the gut, and these environmental changes result in various bacterial infections and chronic enteric inflammatory diseases. Here, we illustrate how antibiotics are associated with an increased risk of antibiotic-associated diseases by driving intestinal environment changes that favor the proliferation and virulence of pathogens. Understanding the pathogenesis caused by antibiotics would be a crucial key to the treatment of antibiotic-associated diseases by mitigating changes in the intestinal environment and restoring it to its original state.

Early bacterial biofilm colonizers in the coastal waters of Mauritius

Background: The past years have witnessed a growing number of researches in biofilm forming communities due to their environmental and maritime industrial implications. To gain a better understanding of the early bacterial biofilm community, microfiber nets were used as artificial substrates and incubated for a period of 24 h in Mauritian coastal waters. Next-generation sequencing technologies were employed as a tool for identification of early bacterial communities. Different genes associated with quorum sensing and cell motility were further investigated. Results: Proteobacteria were identified as the predominant bacterial microorganisms in the biofilm within the 24 h incubation, of which members affiliated to Gammaproteobacteria, Alphaproteobacteria and Betaproteobacteria were among the most abundant classes. The biofilm community patterns were also driven by phyla such as Firmicutes, Bacteroidetes, Chloroflexi, Actinobacteria and Verrucomicrobia. The functional analysis based on KEGG classification indicated high activities in carbohydrate, lipid and amino acids metabolism. Different genes encoding for luxI, lasI, agrC, flhA, cheA and cheB showed the involvement of microbial members in quorum sensing and cell motility. Conclusion: This study provides both an insight on the early bacterial biofilm forming community and the genes involved in quorum sensing and bacterial cell motility.

Rhizobacterial characterization for quality control of eucalyptus biogrowth promoter products

Abstract Plant growth-promoting rhizobacteria strains from special formulations have been used to optimize eucalyptus cutting production. To undertake quality control for the formulated products, the rhizobacterial strains should be characterized to assess their purity and authentication. In the present study, we characterized nine strains of rhizobacteria, including three Bacillus subtilis (S1, S2 and 3918), two Pseudomonas sp. (MF4 and FL2), P. putida (MF2), P. fulva (Ca), Frateuria aurantia (R1), and Stenotrophomonas maltophilia (CIIb). The strains were differentiated by colony morphology after 24 h of incubation in three different solid state culture media (glucose-nutritive agar, 523 medium and yeast extract-mannitol agar), sensitivity to a panel of 28 antibiotics (expressed according to the formation of inhibition halos of bacterial growth in the presence of antibiotics), and PCR-RFLP profiles of the 16S rDNA gene produced using nine restriction enzymes. It was possible to differentiate all nine strains of rhizobacteria using their morphological characteristics and sensitivity to antibiotics. The molecular analysis allowed us to separate the strains CIIb, FL2 and R1 from the strains belonging to the genera Bacillus and Pseudomonas. By using these three methods concomitantly, we were able to determine strain purity and perform the authentication.

Symbiont modulates expression of specific gene categories in Angomonas deanei

Trypanosomatids are parasites that cause disease in humans, animals, and plants. Most are non-pathogenic and some harbor a symbiotic bacterium. Endosymbiosis is part of the evolutionary process of vital cell functions such as respiration and photosynthesis. Angomonas deanei is an example of a symbiont-containing trypanosomatid. In this paper, we sought to investigate how symbionts influence host cells by characterising and comparing the transcriptomes of the symbiont-containing A. deanei (wild type) and the symbiont-free aposymbiotic strains. The comparison revealed that the presence of the symbiont modulates several differentially expressed genes. Empirical analysis of differential gene expression showed that 216 of the 7625 modulated genes were significantly changed. Finally, gene set enrichment analysis revealed that the largest categories of genes that downregulated in the absence of the symbiont were those involved in oxidation-reduction process, ATP hydrolysis coupled proton transport and glycolysis. In contrast, among the upregulated gene categories were those involved in proteolysis, microtubule-based movement, and cellular metabolic process. Our results provide valuable information for dissecting the mechanism of endosymbiosis in A. deanei.

Actividad antibacteriana in vitro de Curcuma longa (Zingiberaceae) frente a bacterias nosocomiales en Montería, Colombia / In vitro antibacterial activity of Curcuma longa (Zingiberaceae) against nosocomial bacteria in Montería, Colombia

ResumenLa resistencia bacteriana es un problema de salud creciente a nivel mundial que genera graves impactos económicos y sociales, comprometiendo la acción terapéutica de los antibióticos actuales. Por ello, la búsqueda de nuevos compuestos con propiedades antimicrobianas se hace más relevante en los estudios modernos, en especial frente a bacterias de interés clínico. En el presente estudio se evaluó la actividad antibacteriana in vitro del extracto etanólico y el aceite esencial de Curcuma longa L (Zingiberaceae), contra bacterias nosocomiales utilizando el método de microdilución. Se utilizaron cepas de Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, Proteus sp., Salmonella sp. y Bacillus sp., aisladas de infecciones nosocomiales en un centro hospitalario de la ciudad de Montería y cepas de referencia de S. aureus ATCC 43300, S. aureus ATCC 29213, S. aureus ATCC 25923, P. aeruginosa ATCC 27853, E. coli ATCC 25922 y K. pneumoniae ATCC 700603. El perfil antibacterial del extracto etanólico fue más evidente a las concentraciones más altas (1 000 ppm), obteniendo porcentajes de reducción significativos de más del 50 % frente a K. pneumoniae ATCC 700603 y un aislado clínico de E. coli, mientras que, frente al aislado clínico del género Bacillus fue más activo el aceite esencial. Para el resto de los microorganismos los porcentajes de reducción obtenidos a una concentración de 1 000 ppm variaron entre 17 y 42 % con el extracto etanólico y entre 8 y 43 % con el aceite esencial. A concentraciones de 100 y 500 ppm la actividad antibacteriana de los extractos fue menor. Los resultados obtenidos indican que el extracto etanólico y el aceite esencial de los rizomas de C. longa poseen compuestos activos con propiedades antibacterianas que podrían emplearse en investigaciones futuras, como una alternativa terapéutica para el tratamiento de infecciones producidas por patógenos nosocomiales.

Abstract:Bacterial resistance is a growing health problem worldwide that has serious economic and social impacts, compromising public health, and the therapeutic action of current antibiotics. Therefore, the search for new compounds with antimicrobial properties is relevant in modern studies, particularly against bacteria of clinical interest. In the present study, in vitro antibacterial activity of the ethanol extract and essential oil of Curcuma longa (Zingiberaceae) was evaluated against nosocomial bacteria, using the microdilution method. Escherichia coli strains, Pseudomonas aeruginosa, Klebsiella pneumoniae, Proteus sp. were used, Salmonella sp. and Bacillus sp., isolated from nosocomial infections in a hospital in the city of Monteria and reference strains of S. aureus ATCC 43300, S. aureus ATCC 29213, S. aureus ATCC 25923, P. aeruginosa ATCC 27853, E. coli ATCC 25922 and K. pneumonia ATCC 700603. The ethanol extract antibacterial profile was more efficient at higher concentrations (1 000 ppm), obtaining significant percentages of reduction of more than 50 % against K. pneumoniae ATCC 700603 and a clinical isolate of E. coli; while compared to Bacillus clinical isolate, was more active than the essential oil. For the rest of microorganisms, the reduction percentages obtained at a concentration of 1 000 ppm varied between 17 and 42 % with ethanolic extract, and 8 to 43 % with essential oil. At concentrations of 100 and 500 ppm antibacterial activity of the extracts was lower. The results indicated that the ethanolic extract and essential oil of C. longa rhizomes have active compounds with antibacterial properties that could be used in future research as a therapeutic alternative for the treatment of infections caused by nosocomial pathogens. Rev. Biol. Trop. 64 (3): 1201-1208. Epub 2016 September 01.

Habitat conditions drive phylogenetic structure of dominant bacterial phyla of microbialite communities from several locations in Mexico / Las condiciones del hábitat determinan la estructura filogenética de filos (phyla) bacterianos dominantes de comunidades de microbialitos de diferentes regiones en México

Abstract:Community structure and composition are dictated by evolutionary and ecological assembly processes which are manifested in signals of, species diversity, species abundance and species relatedness. Analysis of species coexisting relatedness, has received attention as a tool to identify the processes that influence the composition of a community within a particular habitat. In this study, we tested if microbialite genetic composition is dependent on random events versus biological/abiotical factors. This study was based on a large genetic data set of two hypervariable regions (V5 and V6) from previously generated barcoded 16S rRNA amplicons from nine microbialite communities distributed in Northeastern, Central and Southeastern Mexico collected in May and June of 2009. Genetic data of the most abundant phyla (Proteobacteria, Planctomycetes, Verrucomicrobia, Bacteroidetes, and Cyanobacteria) were investigated in order to state the phylogenetic structure of the complete communities as well as each phylum. For the complete dataset, Webb NTI index showed positive and significant values in the nine communities analysed, where values ranged from 31.5 in Pozas Azules I to 57.2 in Bacalar Pirate Channel; meanwhile, NRI index were positive and significant in six of the nine communities analysed with values ranging from 18.1 in Pozas Azules I to 45.1 in Río Mesquites. On the other hand, when comparing each individual phylum, NTI index were positive and significant in all groups, except in Cyanobacteria for which positive and significant values were only found in three localities; finally, NRI index was significant in only a few of the comparisons performed. The results suggest that habitat filtering is the main process that drives phylogenetic structure in bacterial communities associated to microbialites with the exception of Cyanobacteria where different lineages can contribute to microbialite formation and growth. Rev. Biol. Trop. 64 (3): 10571065. Epub 2016 September 01.

ResumenLa estructura y composición de las comunidades son determinadas por procesos evolutivos y ecológicos que se manifiestan en señales de diversidad, abundancia y la relación de especies. El análisis de la relación de especies que coexisten ha recibido atención como una herramienta para identificar los procesos que influyen en la composición de una comunidad dentro de un hábitat particular. En este estudio, evaluamos si la composición genética de bacterias microbialíticas depende de acontecimientos al azar vs factores biológicos/ abióticos. Este estudio se basa en un conjunto de datos genéticos de dos regiones hipervariables (V5 y V6) de gen 16S rRNA generados previamente de nueve comunidades de microbialitos distribuidos en el Noreste, Centro y Sureste de México, recolectados en mayo y junio 2009. Los datos genéticos de los filos más abundantes (Proteobacteria, Planctomycetes, Verrucomicrobia, Bacteroidetes y Cyanobacteria) fueron analizados para determinar la estructura filogenética de la comunidad y de cada filo por separado. Para el análisis conjunto, el índice NTI de Webb mostró valores positivos y significativos en las nueve comunidades analizadas, en donde los valores oscilaron entre 31.5 en Pozas Azules I y 57.2 en el Canal Pirata en Bacalar; en contraste, los valores del índice NRI fueron positivos y significativos en seis de las nueve comunidades analizadas con valores oscilando desde 18.1 en Pozas Azules I hasta 45.1 en Río Mezquites. Por otro lado, en la comparación de cada filo individual, el índice NTI fue positivo y significativo en todos los grupos excepto en Cyanobacteria, en donde valores positivos y significativos fueron encontrados sólo en tres localidades; finalmente, el índice NRI fue significativo sólo en unas cuantas de las comparaciones realizadas. Los resultados sugieren que el filtrado del hábitat es el proceso principal que determina la estructura filogenética de las comunidades bacterianas asociadas a microbialitos con la excepción de las cianobacterias en donde diferentes linajes pueden contribuir a la formación y crecimiento del microbialito.